Variant report

Variant	rs11689688
Chromosome Location	chr2:39416457-39416458
allele	A/C
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	REST	chr2:39416126-39416551	SK-N-SH	brain:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
2	REST	chr2:39416067-39416506	HCT-116	colon:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
3	REST	chr2:39416081-39416485	HepG2	liver:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
4	REST	chr2:39415913-39416532	ECC-1	luminal epithelium:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
5	REST	chr2:39416109-39416489	Hela-S3	cervix:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
6	POLR2A	chr2:39416206-39416490	MCF10A-Er-Src	breast:	n/a	n/a
7	REST	chr2:39416181-39416488	PFSK-1	brain:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
8	REST	chr2:39415961-39416657	ECC-1	luminal epithelium:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
9	MXI1	chr2:39415962-39416501	IMR90	lung:	n/a	n/a
10	REST	chr2:39416144-39416461	H1-hESC	embryonic stem cell:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
11	REST	chr2:39415932-39416578	MCF-7	breast:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
12	REST	chr2:39416020-39416575	PFSK-1	brain:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
13	TEAD4	chr2:39416109-39416553	A549	lung:	n/a	n/a
14	REST	chr2:39416083-39416571	MCF-7	breast:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
15	REST	chr2:39416092-39416537	PANC-1	pancreas:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
16	REST	chr2:39416190-39416460	SK-N-SH	brain:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
17	GATA2	chr2:39416352-39416847	SH-SY5Y	brain:	n/a	n/a
18	BATF	chr2:39416281-39416512	GM12878	blood:	n/a	n/a
19	REST	chr2:39416002-39416532	A549	lung:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
20	REST	chr2:39415999-39416652	HL-60	blood:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
21	REST	chr2:39416163-39416519	HCT-116	colon:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
22	REST	chr2:39416011-39416533	PANC-1	pancreas:	n/a	chr2:39416310-39416323 chr2:39416291-39416300
23	REST	chr2:39416084-39416490	PFSK-1	brain:	n/a	chr2:39416310-39416323 chr2:39416291-39416300

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39403902..39406295-chr2:39414907..39416549,2	MCF-7	breast:

Variant related genes	Relation type
CDKL4	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10175855	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10194771	0.88[AMR][1000 genomes]
rs10196407	0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10427162	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs10865146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11124661	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11124663	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11124664	0.87[AMR][1000 genomes]
rs11673802	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11677985	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12165133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12712631	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712633	0.84[MEX][hapmap];0.91[AMR][1000 genomes]
rs13000581	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13005378	0.82[CHB][hapmap]
rs13028683	0.88[CHB][hapmap]
rs17023372	0.88[GIH][hapmap]
rs1976594	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2136638	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2373527	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs2708222	0.94[GIH][hapmap]
rs2708223	0.94[GIH][hapmap];0.83[MEX][hapmap]
rs4350721	0.81[ASN][1000 genomes]
rs4670917	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6544209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6544211	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6743345	0.90[MEX][hapmap];0.85[AMR][1000 genomes]
rs6753194	0.92[EUR][1000 genomes]
rs6761679	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7562981	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7563373	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7563858	1.00[EUR][1000 genomes]
rs7569834	0.88[GIH][hapmap];0.84[MEX][hapmap]
rs7573535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7575216	0.91[GIH][hapmap];0.84[MEX][hapmap]
rs7583170	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs7584676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7590889	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7594004	0.92[EUR][1000 genomes]
rs7596120	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv1000658	chr2:39374206-39466374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39401800-39422600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:39406200-39429800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:39411000-39423000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:39411000-39423200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:39411000-39448400	Weak transcription	HSMMtube	muscle

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