Variant report

Variant	rs12440928
Chromosome Location	chr15:57771387-57771388
allele	C/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	chr15:57771289-57771436	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000261489	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10220805	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10518923	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775165	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs10851614	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10851615	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10851616	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs10851617	0.88[EUR][1000 genomes]
rs11071323	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11071324	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11071325	0.88[EUR][1000 genomes]
rs11071326	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs11630712	0.88[EUR][1000 genomes]
rs11630713	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs11630740	0.88[EUR][1000 genomes]
rs11631943	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11634739	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs11637220	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637265	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12323972	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12437888	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12438901	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439099	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs12439126	0.88[EUR][1000 genomes]
rs12441608	0.91[EUR][1000 genomes]
rs12442969	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12592077	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12593650	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs12593685	0.89[EUR][1000 genomes]
rs12593721	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595135	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs12595169	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1280381	0.96[ASN][1000 genomes]
rs1280387	0.86[EUR][1000 genomes]
rs1280412	1.00[YRI][hapmap]
rs16977531	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16977534	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16977558	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs16977560	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs16977561	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs16977567	0.80[EUR][1000 genomes]
rs1980048	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs2087981	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2131740	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs2172613	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs2414510	0.85[EUR][1000 genomes]
rs2942043	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4545749	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs58161678	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58253526	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164486	0.88[EUR][1000 genomes]
rs7496403	0.88[EUR][1000 genomes]
rs932028	0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs932029	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs955206	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs966693	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv569579	chr15:57622600-57775806	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2751536	chr15:57627408-57788408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1038663	chr15:57633015-57786420	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1045486	chr15:57633015-57786592	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv904252	chr15:57635719-57775806	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv569581	chr15:57635719-57775826	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv904253	chr15:57635719-57781038	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1038144	chr15:57642065-57778324	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1041346	chr15:57642065-57779035	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1037339	chr15:57642065-57781565	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv569583	chr15:57643653-57775826	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1054095	chr15:57643653-57778324	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv2761873	chr15:57643653-57779035	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1043074	chr15:57643653-57779035	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv1036911	chr15:57643653-57781565	Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv569584	chr15:57644267-57775806	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv1037376	chr15:57644267-57775826	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv457166	chr15:57644267-57775826	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv569585	chr15:57644267-57775826	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv1045506	chr15:57644267-57779035	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv516366	chr15:57644267-57781038	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv457170	chr15:57644456-57790436	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv569588	chr15:57644456-57790436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv1040066	chr15:57647132-57781565	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv457171	chr15:57648012-57782249	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	nsv569589	chr15:57648012-57782249	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	nsv1050158	chr15:57655776-57779035	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Genic 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	4 gene(s)	inside rSNPs	diseases
30	nsv833022	chr15:57657412-57830112	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
31	nsv1045620	chr15:57680733-57804237	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57749800-57787400	Weak transcription	Ovary	ovary
2	chr15:57767200-57772400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr15:57767400-57772200	Weak transcription	Esophagus	oesophagus
4	chr15:57767600-57771600	Enhancers	Fetal Kidney	kidney
5	chr15:57769000-57771800	Enhancers	Fetal Intestine Small	intestine
6	chr15:57769200-57771600	Enhancers	Fetal Intestine Large	intestine
7	chr15:57769200-57772600	Enhancers	Pancreas	Pancrea
8	chr15:57769400-57771600	Enhancers	Stomach Mucosa	stomach
9	chr15:57769600-57773400	Weak transcription	NHEK	skin
10	chr15:57769800-57771400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:57769800-57771600	Strong transcription	Fetal Stomach	stomach
12	chr15:57770000-57773400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:57770000-57773400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:57770200-57778000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr15:57770200-57778800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr15:57770400-57773000	Weak transcription	HMEC	breast
17	chr15:57770400-57780200	Weak transcription	Fetal Heart	heart
18	chr15:57770800-57771400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr15:57770800-57771400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr15:57770800-57772000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:57770800-57772200	Enhancers	Liver	Liver
22	chr15:57770800-57772800	Enhancers	HepG2	liver
23	chr15:57770800-57775400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:57770800-57777000	Weak transcription	HUVEC	blood vessel
25	chr15:57770800-57778000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr15:57771000-57771400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:57771000-57771800	Enhancers	Aorta	Aorta
28	chr15:57771000-57773400	Weak transcription	Fetal Lung	lung
29	chr15:57771000-57777400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr15:57771000-57777600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:57771000-57778000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:57771000-57778000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:57771000-57778600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:57771000-57795200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:57771200-57771800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:57771200-57777800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr15:57771200-57778000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:57771200-57778200	Weak transcription	Lung	lung

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