Variant report

Variant	rs11125075
Chromosome Location	chr2:46656344-46656345
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:13)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:46655752-46656716	K562	blood:	n/a	n/a
2	MYC	chr2:46656154-46656358	K562	blood:	n/a	n/a
3	IRF1	chr2:46655775-46656697	K562	blood:	n/a	n/a
4	YY1	chr2:46655880-46656563	K562	blood:	n/a	chr2:46656237-46656259
5	MAX	chr2:46655902-46656561	K562	blood:	n/a	n/a
6	POLR2A	chr2:46655721-46656595	K562	blood:	n/a	n/a
7	MYC	chr2:46655849-46656842	K562	blood:	n/a	n/a
8	BHLHE40	chr2:46656018-46656527	K562	blood:	n/a	chr2:46656228-46656244
9	MAZ	chr2:46655920-46656530	K562	blood:	n/a	n/a
10	IRF1	chr2:46655471-46656652	K562	blood:	n/a	n/a
11	HMGN3	chr2:46655990-46656387	K562	blood:	n/a	n/a
12	YY1	chr2:46655799-46656561	K562	blood:	n/a	chr2:46656237-46656259
13	ELF1	chr2:46655990-46656404	K562	blood:	n/a	chr2:46656022-46656034
14	ETS1	chr2:46655965-46656557	K562	blood:	n/a	chr2:46656240-46656253
15	HEY1	chr2:46655741-46656673	K562	blood:	n/a	chr2:46656024-46656039
16	RCOR1	chr2:46655938-46656510	K562	blood:	n/a	n/a
17	TAF1	chr2:46655741-46656558	K562	blood:	n/a	n/a
18	TEAD4	chr2:46655624-46656734	K562	blood:	n/a	n/a
19	GABPA	chr2:46655982-46656451	K562	blood:	n/a	n/a
20	MXI1	chr2:46656183-46656593	K562	blood:	n/a	n/a
21	ELF1	chr2:46655873-46656412	K562	blood:	n/a	chr2:46656022-46656034
22	TBL1XR1	chr2:46656099-46656578	K562	blood:	n/a	n/a
23	CEBPB	chr2:46656315-46656593	K562	blood:	n/a	n/a
24	MAX	chr2:46655848-46656962	K562	blood:	n/a	n/a
25	GABPA	chr2:46655904-46656417	K562	blood:	n/a	n/a
26	STAT5A	chr2:46655884-46656591	K562	blood:	n/a	n/a
27	PML	chr2:46655907-46656671	K562	blood:	n/a	n/a
28	USF1	chr2:46656002-46656410	K562	blood:	n/a	chr2:46656228-46656244
29	CCNT2	chr2:46655876-46656503	K562	blood:	n/a	n/a
30	CEBPB	chr2:46656316-46656664	HepG2	liver:	n/a	n/a
31	E2F6	chr2:46656040-46656386	K562	blood:	n/a	chr2:46656255-46656265
32	ZNF143	chr2:46656202-46656535	K562	blood:	n/a	n/a
33	TAF1	chr2:46655756-46656592	K562	blood:	n/a	n/a
34	POLR2A	chr2:46655729-46656622	K562	blood:	n/a	n/a
35	IRF1	chr2:46655989-46656539	K562	blood:	n/a	n/a
36	POLR2A	chr2:46655803-46656541	K562	blood:	n/a	n/a
37	ZNF384	chr2:46655896-46656553	K562	blood:	n/a	n/a
38	EGR1	chr2:46656013-46656378	K562	blood:	n/a	n/a
39	POLR2A	chr2:46655737-46656609	K562	blood:	n/a	n/a
40	CHD2	chr2:46655799-46656484	K562	blood:	n/a	n/a
41	SIN3AK20	chr2:46655865-46656498	K562	blood:	n/a	n/a
42	UBTF	chr2:46655780-46656570	K562	blood:	n/a	n/a
43	TBP	chr2:46655740-46656715	K562	blood:	n/a	n/a
44	PML	chr2:46655804-46656645	K562	blood:	n/a	n/a
45	SP2	chr2:46656129-46656344	K562	blood:	n/a	n/a
46	EP300	chr2:46655808-46656481	K562	blood:	n/a	chr2:46656142-46656158 chr2:46656227-46656243
47	POLR2A	chr2:46655763-46656630	K562	blood:	n/a	n/a
48	TEAD4	chr2:46655901-46656547	K562	blood:	n/a	n/a
49	GTF2B	chr2:46656030-46656568	K562	blood:	n/a	n/a
50	JUND	chr2:46655996-46656531	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46656214..46657827-chr2:46704173..46707018,3	K562	blood:
2	chr2:46655601..46658738-chr2:47401405..47405423,5	K562	blood:
3	chr2:46524680..46526500-chr2:46655060..46657015,2	K562	blood:
4	chr2:46654722..46656648-chr2:47126320..47128240,2	K562	blood:

(count:13 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC018682.6.1-1	chr2:46656276-46656418	XLOC_001455
2	lnc-AC018682.6.1-1	chr2:46656287-46656418	XLOC_001455
3	lnc-AC018682.6.1-1	chr2:46656276-46656418	XLOC_001455
4	lnc-AC018682.6.1-1	chr2:46656276-46656418	XLOC_001455
5	lnc-AC018682.6.1-1	chr2:46656334-46656418	XLOC_001455
6	lnc-AC018682.6.1-1	chr2:46656276-46656418	XLOC_001455
7	lnc-AC018682.6.1-1	chr2:46656287-46656418	XLOC_001455
8	lnc-AC018682.6.1-1	chr2:46656276-46656418	XLOC_001455
9	lnc-AC018682.6.1-1	chr2:46656276-46656418	XLOC_001455
10	lnc-AC018682.6.1-1	chr2:46656276-46656418	XLOC_001455
11	lnc-AC018682.6.1-1	chr2:46656259-46656418	NONHSAT070485
12	lnc-AC018682.6.1-1	chr2:46656334-46656418	NONHSAT070496
13	lnc-AC018682.6.1-1	chr2:46656329-46656418	NONHSAT147087

No data

Variant related genes	Relation type
TMEM247	TF binding region
ENSG00000143933	Chromatin interaction
ENSG00000228925	Chromatin interaction
ENSG00000116016	Chromatin interaction
ENSG00000187600	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12619985	0.84[CEU][hapmap]
rs12986653	1.00[JPT][hapmap]
rs12986899	0.98[ASN][1000 genomes]
rs12991646	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13003074	0.96[ASN][1000 genomes]
rs13010062	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13010097	1.00[JPT][hapmap]
rs13030579	1.00[JPT][hapmap]
rs1447563	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[ASN][1000 genomes]
rs1530621	0.81[MEX][hapmap];0.84[TSI][hapmap]
rs1530624	0.98[ASN][1000 genomes]
rs2084679	1.00[JPT][hapmap]
rs2121698	0.81[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs2121700	0.93[GIH][hapmap]
rs2346177	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs2346414	1.00[JPT][hapmap]
rs2346415	1.00[JPT][hapmap]
rs34712412	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34791442	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35462976	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4396767	1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4563285	0.96[ASN][1000 genomes]
rs4953365	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4953371	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4953372	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4953379	0.96[ASN][1000 genomes]
rs4953388	1.00[JPT][hapmap]
rs56048837	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv457330	chr2:46637081-46660752	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv581744	chr2:46637081-46660752	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1001902	chr2:46651624-46675665	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv997637	chr2:46651624-46676628	Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv1003646	chr2:46651624-46677186	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11125075	CRIPT	cis	multi-tissue	Pritchard
rs11125075	CRIPT	cis	parietal	SCAN
rs11125075	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs11125075	CRIPT	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46647800-46658400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:46653600-46657600	Active TSS	K562	blood
3	chr2:46655600-46657600	Active TSS	Placenta	Placenta
4	chr2:46656000-46656400	ZNF genes & repeats	Aorta	Aorta
5	chr2:46656000-46656600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:46656200-46656600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:46656200-46656600	Enhancers	Esophagus	oesophagus

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