Variant report

Variant	rs13317939
Chromosome Location	chr3:78990535-78990536
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	chr3:78989798-78990571	PFSK-1	brain:	n/a	n/a
2	RCOR1	chr3:78990353-78991709	IMR90	lung:	n/a	n/a
3	FOS	chr3:78990390-78991169	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr3:78990499-78991169	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
RN7SL751P	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1031933	1.00[CHD][hapmap]
rs10511126	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs10514741	0.88[YRI][hapmap]
rs13321050	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs13321792	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs13321973	0.86[AFR][1000 genomes]
rs13322089	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325291	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325521	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1480685	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1480686	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs162819	1.00[CEU][hapmap]
rs162873	1.00[CEU][hapmap]
rs162875	1.00[CEU][hapmap]
rs167944	1.00[CEU][hapmap]
rs17016495	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs17016507	1.00[CEU][hapmap]
rs17016511	1.00[CEU][hapmap]
rs17016573	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17016593	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17016641	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs17016648	0.92[YRI][hapmap]
rs17016656	1.00[CHD][hapmap];0.81[YRI][hapmap]
rs2125123	1.00[CEU][hapmap]
rs2271575	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28412538	0.83[AFR][1000 genomes]
rs28431826	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564735	1.00[EUR][1000 genomes]
rs28611062	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28667917	0.87[AFR][1000 genomes]
rs331132	1.00[CEU][hapmap]
rs331133	1.00[CEU][hapmap]
rs331159	1.00[CEU][hapmap]
rs333499	1.00[CEU][hapmap]
rs58608513	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59931439	0.92[EUR][1000 genomes]
rs72904273	0.92[EUR][1000 genomes]
rs72904277	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72906141	0.92[EUR][1000 genomes]
rs72906176	0.86[AFR][1000 genomes]
rs72910206	0.87[AFR][1000 genomes]
rs72910208	0.85[AFR][1000 genomes]
rs72910224	0.86[AFR][1000 genomes]
rs9631526	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809330	0.85[AFR][1000 genomes]
rs9818387	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs9822620	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829918	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9832632	1.00[CHD][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap]
rs9835586	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9836486	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9838831	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs9839144	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839572	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9842144	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853126	0.92[YRI][hapmap]
rs9858080	0.86[AFR][1000 genomes]
rs9868575	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870336	0.92[YRI][hapmap]
rs9871957	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876637	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9880690	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv966945	chr3:78990076-78992480	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78963200-78991000	Weak transcription	Fetal Brain Male	brain
2	chr3:78967200-79000600	Weak transcription	Fetal Kidney	kidney
3	chr3:78969000-78990800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:78969000-78991000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:78969600-79000600	Weak transcription	HepG2	liver
6	chr3:78970400-78991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:78977200-78990800	Weak transcription	Psoas Muscle	Psoas
8	chr3:78978400-78992200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:78978800-78990800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:78981600-78991600	Weak transcription	Fetal Heart	heart
11	chr3:78982400-79001800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:78986000-78990600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:78986000-78990800	Weak transcription	NHLF	lung
14	chr3:78986200-78990800	Weak transcription	Primary T cells from cord blood	blood
15	chr3:78986800-78992200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:78988000-78990600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:78988000-78991000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:78988000-78993600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:78988000-79002400	Weak transcription	Aorta	Aorta
20	chr3:78988200-78990800	Weak transcription	Fetal Stomach	stomach
21	chr3:78988200-78992800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:78988400-78990800	Weak transcription	Fetal Lung	lung
23	chr3:78988400-78991200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:78988400-78991400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:78988400-78992400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:78989200-78991000	Enhancers	Colon Smooth Muscle	Colon
27	chr3:78989600-78991000	Enhancers	Rectal Smooth Muscle	rectum
28	chr3:78989600-78991600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:78990000-78991600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:78990200-78991400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:78990200-78991600	Enhancers	Osteobl	bone
32	chr3:78990400-78991400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:78990400-78991400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:78990400-78991400	Enhancers	NHDF-Ad	bronchial
35	chr3:78990400-78991600	Enhancers	NHEK	skin
36	chr3:78990400-78992000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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