Variant report

Variant	rs2049043
Chromosome Location	chr9:139877129-139877130
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:139876039-139877532	Hela-S3	cervix:	n/a	n/a
2	SMC3	chr9:139876174-139877552	Hela-S3	cervix:	n/a	chr9:139876445-139876452 chr9:139876757-139876767
3	GTF2F1	chr9:139876548-139877556	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr9:139877123-139877267	Hela-S3	cervix:	n/a	n/a
5	TCF7L2	chr9:139877046-139877677	Hela-S3	cervix:	n/a	chr9:139877469-139877479
6	TBP	chr9:139876458-139877401	Hela-S3	cervix:	n/a	n/a
7	RCOR1	chr9:139877055-139877555	Hela-S3	cervix:	n/a	n/a
8	MXI1	chr9:139877076-139877457	Hela-S3	cervix:	n/a	n/a
9	TFAP2A	chr9:139876263-139877717	Hela-S3	cervix:	n/a	chr9:139876546-139876556 chr9:139876942-139876953 chr9:139877292-139877303 chr9:139876546-139876556 chr9:139877290-139877304 chr9:139877292-139877303 chr9:139876475-139876484 chr9:139877292-139877303 chr9:139876942-139876953 chr9:139877288-139877303 chr9:139877292-139877303 chr9:139876546-139876556 chr9:139876942-139876953
10	ELK4	chr9:139876581-139877361	Hela-S3	cervix:	n/a	n/a
11	MAX	chr9:139876970-139877512	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr9:139877123-139877382	Hela-S3	cervix:	n/a	n/a
13	NR3C1	chr9:139876633-139877289	A549	lung:	n/a	chr9:139876900-139876914 chr9:139876760-139876773 chr9:139876913-139876928 chr9:139876899-139876915 chr9:139876899-139876915 chr9:139876899-139876915 chr9:139876900-139876914
14	MYC	chr9:139876101-139877446	Hela-S3	cervix:	n/a	n/a
15	TFAP2C	chr9:139875642-139877728	Hela-S3	cervix:	n/a	chr9:139877288-139877303
16	MAX	chr9:139876147-139877507	Hela-S3	cervix:	n/a	n/a
17	NR3C1	chr9:139876697-139877131	A549	lung:	n/a	chr9:139876900-139876914 chr9:139876760-139876773 chr9:139876913-139876928 chr9:139876899-139876915 chr9:139876899-139876915 chr9:139876899-139876915 chr9:139876900-139876914
18	ZNF143	chr9:139876779-139877395	Hela-S3	cervix:	n/a	n/a
19	ZKSCAN1	chr9:139877089-139877539	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr9:139877057-139877396	Hela-S3	cervix:	n/a	n/a
21	NFYA	chr9:139877096-139877411	Hela-S3	cervix:	n/a	n/a
22	NR3C1	chr9:139876621-139877188	A549	lung:	n/a	chr9:139876900-139876914 chr9:139876760-139876773 chr9:139876913-139876928 chr9:139876899-139876915 chr9:139876899-139876915 chr9:139876899-139876915 chr9:139876900-139876914
23	BRCA1	chr9:139877058-139877367	Hela-S3	cervix:	n/a	n/a
24	MAZ	chr9:139876119-139877478	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:139701574..139704508-chr9:139876130..139878541,2	MCF-7	breast:
2	chr9:139873674..139878101-chr9:139922042..139924595,3	K562	blood:
3	chr9:139841985..139846327-chr9:139875508..139880293,6	MCF-7	breast:
4	chr9:139837657..139841229-chr9:139875890..139877651,3	MCF-7	breast:

Variant related genes	Relation type
LCNL1	TF binding region
ENSG00000184925	Chromatin interaction
ENSG00000176919	Chromatin interaction
ENSG00000159069	Chromatin interaction
ENSG00000107331	Chromatin interaction
ENSG00000196642	Chromatin interaction
ENSG00000228544	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10114487	0.81[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap]
rs10124249	0.82[ASN][1000 genomes]
rs10781529	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10781530	0.86[CEU][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10870154	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10870155	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10870157	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10870158	0.94[ASW][hapmap];0.86[CEU][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10870159	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12340777	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12343591	0.93[ASN][1000 genomes]
rs12343713	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12350318	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17578859	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2049040	0.83[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2049041	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271862	0.94[ASW][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.81[EUR][1000 genomes]
rs2271863	0.96[MEX][hapmap]
rs28609008	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3814499	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3814500	0.95[CEU][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3814501	0.95[CEU][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3829902	0.91[JPT][hapmap]
rs4355883	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4576515	0.80[AMR][1000 genomes]
rs4880082	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4880180	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4880182	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56030643	0.90[ASN][1000 genomes]
rs6560653	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6926	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs7022347	0.80[AMR][1000 genomes]
rs7029565	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048567	0.81[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7388671	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7470867	0.94[ASW][hapmap];0.82[CEU][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7849705	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7854838	0.84[EUR][1000 genomes]
rs7860430	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs867250	0.82[ASN][1000 genomes]
rs867251	0.95[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:69 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv540342	chr9:139218422-139973312	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	317 gene(s)	inside rSNPs	diseases
2	nsv469918	chr9:139254317-140068342	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	341 gene(s)	inside rSNPs	diseases
3	nsv540346	chr9:139360142-140164011	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	471 gene(s)	inside rSNPs	diseases
4	nsv1039149	chr9:139376829-139991102	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	303 gene(s)	inside rSNPs	diseases
5	esv1803979	chr9:139395473-139979276	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	267 gene(s)	inside rSNPs	diseases
6	esv1831778	chr9:139395473-139979276	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	267 gene(s)	inside rSNPs	diseases
7	esv1821575	chr9:139395473-140068342	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
8	esv2422220	chr9:139478587-140244550	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	454 gene(s)	inside rSNPs	diseases
9	nsv894442	chr9:139544437-140462099	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
10	nsv894451	chr9:139598108-139995065	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	200 gene(s)	inside rSNPs	diseases
11	nsv894452	chr9:139598108-140523429	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
12	nsv894454	chr9:139607966-139904037	Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	172 gene(s)	inside rSNPs	diseases
13	nsv894455	chr9:139607966-140411547	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	417 gene(s)	inside rSNPs	diseases
14	nsv818738	chr9:139634495-139904037	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	126 gene(s)	inside rSNPs	diseases
15	nsv894462	chr9:139683224-140274164	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	353 gene(s)	inside rSNPs	diseases
16	nsv894463	chr9:139683224-140411547	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
17	nsv524322	chr9:139690144-140376668	Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	371 gene(s)	inside rSNPs	diseases
18	nsv894469	chr9:139693992-140118448	Bivalent Enhancer Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	200 gene(s)	inside rSNPs	diseases
19	nsv894470	chr9:139693992-140339091	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	358 gene(s)	inside rSNPs	diseases
20	nsv894474	chr9:139694521-140432318	Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
21	nsv540352	chr9:139695108-140351178	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	358 gene(s)	inside rSNPs	diseases
22	nsv894483	chr9:139709976-139963091	Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	119 gene(s)	inside rSNPs	diseases
23	nsv894484	chr9:139709976-140382705	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	360 gene(s)	inside rSNPs	diseases
24	nsv894485	chr9:139709976-140408904	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	363 gene(s)	inside rSNPs	diseases
25	nsv894486	chr9:139725120-140382705	Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	359 gene(s)	inside rSNPs	diseases
26	nsv894487	chr9:139725120-140449582	Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	363 gene(s)	inside rSNPs	diseases
27	esv1803771	chr9:139776400-140274255	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
28	nsv894498	chr9:139810595-140339091	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	324 gene(s)	inside rSNPs	diseases
29	nsv894499	chr9:139810595-140734161	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
30	esv1823828	chr9:139820363-140023694	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	121 gene(s)	inside rSNPs	diseases
31	esv1822764	chr9:139822266-140202692	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	313 gene(s)	inside rSNPs	diseases
32	nsv894500	chr9:139823670-139930945	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	85 gene(s)	inside rSNPs	diseases
33	nsv894501	chr9:139823670-140400275	Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
34	nsv894502	chr9:139823670-140487108	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
35	nsv894503	chr9:139830940-139987350	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
36	esv1834381	chr9:139834195-140031290	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	125 gene(s)	inside rSNPs	diseases
37	esv1823555	chr9:139834714-140362439	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
38	nsv894506	chr9:139841512-140143801	Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	278 gene(s)	inside rSNPs	diseases
39	nsv894507	chr9:139860264-139995065	Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
40	nsv894510	chr9:139860631-139878317	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
41	nsv894511	chr9:139860631-139885820	Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
42	nsv894512	chr9:139860631-139894734	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
43	nsv894513	chr9:139860631-139904037	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
44	nsv894514	chr9:139860631-139943112	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	79 gene(s)	inside rSNPs	diseases
45	nsv894515	chr9:139860631-139963091	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
46	nsv894517	chr9:139860631-139977351	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	diseases
47	nsv894516	chr9:139860631-139979276	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
48	nsv894518	chr9:139860631-139995065	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
49	nsv466690	chr9:139860631-140042320	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	117 gene(s)	inside rSNPs	diseases
50	nsv615989	chr9:139860631-140042320	Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	117 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2049043	C9orf142	cis	cerebellum	SCAN
rs2049043	PHPT1	cis	cerebellum	SCAN
rs2049043	PHPT1	Cis_1M	lymphoblastoid	RTeQTL
rs2049043	MAMDC4	cis	cerebellum	SCAN
rs2049043	VAV2	cis	cerebellum	SCAN
rs2049043	C9orf142	cis	parietal	SCAN
rs2049043	COL5A1	cis	cerebellum	SCAN
rs2049043	RP11-229P13.19	cis	Whole Blood	GTEx
rs2049043	LCNL1	cis	parietal	SCAN
rs2049043	LCN8	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:139872600-139877600	Enhancers	Spleen	Spleen
2	chr9:139873200-139877600	Enhancers	Left Ventricle	heart
3	chr9:139873400-139877600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
4	chr9:139873600-139886200	Weak transcription	Pancreas	Pancrea
5	chr9:139873800-139877200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:139873800-139879600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:139874800-139877600	Enhancers	Placenta	Placenta
8	chr9:139874800-139877600	Enhancers	Right Atrium	heart
9	chr9:139874800-139877800	Enhancers	Lung	lung
10	chr9:139875000-139878400	Flanking Active TSS	Hela-S3	cervix
11	chr9:139875600-139878000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:139875600-139878200	Weak transcription	Brain Angular Gyrus	brain
13	chr9:139875600-139879000	Enhancers	Brain Hippocampus Middle	brain
14	chr9:139876000-139877200	Enhancers	HepG2	liver
15	chr9:139876400-139877400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr9:139876400-139877600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:139876600-139879400	Enhancers	Right Ventricle	heart
18	chr9:139876800-139877400	Bivalent Enhancer	Adipose Nuclei	Adipose
19	chr9:139876800-139877600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
20	chr9:139876800-139879400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:139876800-139880800	Enhancers	Brain Substantia Nigra	brain
22	chr9:139877000-139877200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr9:139877000-139877200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
24	chr9:139877000-139877400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:139877000-139877400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:139877000-139877400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:139877000-139878600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:139877000-139879600	Enhancers	Brain Anterior Caudate	brain
29	chr9:139877000-139879600	Enhancers	Brain Inferior Temporal Lobe	brain

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