Variant report

Variant	rs7631574
Chromosome Location	chr3:48663046-48663047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48662955-48663067	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:48662653-48663059	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:48660022-48663466	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:48662706-48663047	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr3:48662885-48663135	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48661665..48664371-chr3:48687435..48689598,2	MCF-7	breast:
2	chr3:48656876..48658488-chr3:48660227..48663106,2	MCF-7	breast:
3	chr3:48662117..48664677-chr3:48670615..48672606,2	K562	blood:
4	chr3:48662608..48665398-chr3:48666454..48668289,2	K562	blood:
5	chr3:48645535..48647761-chr3:48661454..48663479,2	MCF-7	breast:
6	chr3:48659034..48660590-chr3:48661591..48664038,3	K562	blood:

No data

Variant related genes	Relation type
TMEM89	TF binding region
ENSG00000225697	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000183396	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11706983	1.00[GIH][hapmap];0.87[TSI][hapmap]
rs11708786	1.00[GIH][hapmap]
rs11713694	0.83[GIH][hapmap]
rs11719291	1.00[GIH][hapmap];0.87[TSI][hapmap]
rs12107252	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12107418	1.00[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12715429	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13060933	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13063312	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13070798	0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13074318	0.83[GIH][hapmap]
rs13076269	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13091944	1.00[JPT][hapmap]
rs13096357	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13319651	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13324119	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13324142	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13434258	1.00[GIH][hapmap];0.87[TSI][hapmap]
rs17080289	0.90[CHD][hapmap];1.00[GIH][hapmap];0.84[ASN][1000 genomes]
rs2006871	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276850	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276852	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286651	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2286652	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2302295	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2310996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2310997	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28452701	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2854394	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs34037363	0.83[GIH][hapmap]
rs34096717	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34368826	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34638686	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35064573	1.00[GIH][hapmap];0.87[TSI][hapmap]
rs35343040	0.86[ASN][1000 genomes]
rs35796820	0.84[ASN][1000 genomes]
rs3733086	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821875	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821876	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3969942	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs57334642	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6768448	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6773261	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781283	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6792156	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6792525	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs68042649	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6806059	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs740787	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7620853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809222	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9810549	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9810991	0.89[CHD][hapmap];0.83[GIH][hapmap]
rs9811318	0.88[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9812200	0.94[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9821797	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9830581	0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9836462	0.82[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9837687	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9841602	0.82[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9843316	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9850102	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9851771	0.83[GIH][hapmap]
rs9868809	0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9869698	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9871180	0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9873726	0.86[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9875911	0.83[GIH][hapmap]
rs9878063	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878950	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9881877	0.85[CHD][hapmap];1.00[GIH][hapmap]
rs9882549	1.00[GIH][hapmap]
rs9882962	0.80[CHD][hapmap];0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS 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	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7631574	WDR6	cis	multi-tissue	Pritchard
rs7631574	WDR6	cis	lung	GTEx
rs7631574	USP4	cis	multi-tissue	Pritchard
rs7631574	SLC26A6	cis	lung	GTEx
rs7631574	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs7631574	WDR6	cis	Adipose Subcutaneous	GTEx
rs7631574	WDR6	cis	lymphoblastoid	seeQTL
rs7631574	WDR6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48649000-48672000	Weak transcription	Fetal Brain Male	brain
2	chr3:48656000-48664000	Weak transcription	Brain Germinal Matrix	brain
3	chr3:48656400-48663200	Weak transcription	Hela-S3	cervix
4	chr3:48656400-48664400	Weak transcription	HMEC	breast
5	chr3:48656400-48671400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:48657200-48664600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:48657800-48664200	Weak transcription	Pancreas	Pancrea
8	chr3:48657800-48670000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:48658200-48668000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:48659000-48663600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:48659000-48671200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:48659600-48663200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:48660000-48663600	Weak transcription	Ovary	ovary
14	chr3:48660000-48671200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:48660200-48663200	Weak transcription	Right Ventricle	heart
16	chr3:48660400-48665000	Weak transcription	NHDF-Ad	bronchial
17	chr3:48660400-48667800	Weak transcription	A549	lung
18	chr3:48660600-48663600	Weak transcription	GM12878-XiMat	blood
19	chr3:48660800-48668600	Weak transcription	Fetal Lung	lung
20	chr3:48661000-48663200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:48661000-48671200	Strong transcription	Aorta	Aorta
22	chr3:48661000-48671600	Weak transcription	Psoas Muscle	Psoas
23	chr3:48661200-48670200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:48661200-48670800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:48661200-48671000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr3:48661200-48671800	Weak transcription	Small Intestine	intestine
27	chr3:48661400-48663200	Weak transcription	Brain Angular Gyrus	brain
28	chr3:48661400-48663200	Weak transcription	Brain Substantia Nigra	brain
29	chr3:48661600-48663400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:48661600-48663600	Weak transcription	NH-A	brain
31	chr3:48661600-48664200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:48661600-48664400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:48661600-48670600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:48661600-48670800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:48661600-48670800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:48661600-48670800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:48661600-48670800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr3:48661600-48670800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:48661600-48671200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:48661600-48671400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:48661800-48665000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:48661800-48667400	Strong transcription	Placenta	Placenta
43	chr3:48661800-48670200	Strong transcription	Spleen	Spleen
44	chr3:48661800-48670800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:48661800-48671000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:48661800-48671400	Strong transcription	NHEK	skin
47	chr3:48661800-48671600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:48662000-48663200	Weak transcription	Colonic Mucosa	Colon
49	chr3:48662000-48663400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:48662000-48663800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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