Variant report

Variant	rs399971
Chromosome Location	chr3:50612658-50612659
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	chr3:50612506-50612689	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
2	chr3:50601756..50613871-chr3:50647072..50654542,28	K562	blood:
3	chr3:50606526..50611586-chr3:50612274..50616724,6	MCF-7	breast:

Variant related genes	Relation type
C3orf18	TF binding region
HEMK1	TF binding region
ENSG00000088543	Chromatin interaction
ENSG00000114735	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000114738	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1013233	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1034405	0.89[EUR][1000 genomes]
rs11130252	0.82[EUR][1000 genomes]
rs11716398	0.85[AMR][1000 genomes]
rs11719998	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491425	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12493985	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs129310	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13076850	0.87[EUR][1000 genomes]
rs13083004	0.87[EUR][1000 genomes]
rs13084476	0.82[EUR][1000 genomes]
rs13091933	0.83[EUR][1000 genomes]
rs13094336	0.88[EUR][1000 genomes]
rs1385025	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs175634	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17787569	0.88[EUR][1000 genomes]
rs1971976	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs201193	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201194	0.87[EUR][1000 genomes]
rs201196	0.89[EUR][1000 genomes]
rs201198	0.89[EUR][1000 genomes]
rs2227280	0.88[EUR][1000 genomes]
rs2232248	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232253	0.88[EUR][1000 genomes]
rs2269505	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269507	0.88[EUR][1000 genomes]
rs2355321	0.88[EUR][1000 genomes]
rs2355323	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34202063	0.88[EUR][1000 genomes]
rs34399912	0.88[EUR][1000 genomes]
rs34584636	0.88[EUR][1000 genomes]
rs34756253	0.82[EUR][1000 genomes]
rs34848480	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs34889917	0.88[EUR][1000 genomes]
rs35655236	0.87[EUR][1000 genomes]
rs35690191	0.87[EUR][1000 genomes]
rs35714264	0.83[EUR][1000 genomes]
rs375544	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3792325	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3792328	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3804627	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3804632	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs391620	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3943212	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs396302	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs398703	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs399484	0.84[EUR][1000 genomes]
rs414171	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs417592	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs441516	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443030	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs443436	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs448028	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs453570	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688712	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs490634	0.85[EUR][1000 genomes]
rs59949730	0.88[EUR][1000 genomes]
rs616589	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs628081	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6446212	0.84[AFR][1000 genomes]
rs67588094	0.88[EUR][1000 genomes]
rs6779819	0.84[AMR][1000 genomes]
rs67813889	0.90[EUR][1000 genomes]
rs6784166	0.83[EUR][1000 genomes]
rs6787521	0.87[EUR][1000 genomes]
rs695170	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71326937	0.88[EUR][1000 genomes]
rs728901	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs750453	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs750510	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs751851	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs754298	0.80[EUR][1000 genomes]
rs7635666	0.85[AMR][1000 genomes]
rs7646236	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs808149	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs809454	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs813243	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs900735	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9682401	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9830920	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50607400-50615600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:50607400-50628200	Weak transcription	Small Intestine	intestine
3	chr3:50607600-50613000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:50607600-50614400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:50607600-50617600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:50607600-50628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:50607800-50614200	Weak transcription	Brain Anterior Caudate	brain
8	chr3:50607800-50614800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:50607800-50615200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:50607800-50615200	Weak transcription	Aorta	Aorta
11	chr3:50607800-50620000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:50607800-50628200	Weak transcription	HSMMtube	muscle
13	chr3:50607800-50628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:50608000-50613000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:50608000-50618400	Weak transcription	NH-A	brain
16	chr3:50608000-50621400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:50608000-50621400	Weak transcription	HUVEC	blood vessel
18	chr3:50608000-50621800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:50608200-50612800	Weak transcription	HMEC	breast
20	chr3:50608200-50613800	Weak transcription	Brain Substantia Nigra	brain
21	chr3:50608200-50614000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:50608200-50614200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:50608200-50614400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:50608200-50615200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:50608200-50616200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:50608200-50617400	Weak transcription	Fetal Brain Male	brain
27	chr3:50608200-50624000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:50608200-50628400	Weak transcription	A549	lung
29	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
30	chr3:50608400-50613000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:50608400-50614800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:50608400-50615000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:50608400-50625600	Weak transcription	NHDF-Ad	bronchial
34	chr3:50608800-50614800	Genic enhancers	Placenta	Placenta
35	chr3:50609200-50620800	Strong transcription	Brain Germinal Matrix	brain
36	chr3:50609800-50620600	Strong transcription	Fetal Brain Female	brain
37	chr3:50610000-50613600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:50610000-50614200	Enhancers	Primary T cells fromperipheralblood	blood
39	chr3:50610000-50614400	Weak transcription	Primary B cells from cord blood	blood
40	chr3:50610000-50621400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr3:50610000-50623000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:50610200-50613200	Weak transcription	Fetal Lung	lung
43	chr3:50610200-50614000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:50610200-50614200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:50610200-50614200	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:50610200-50614200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:50610200-50614400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:50610200-50615200	Weak transcription	Left Ventricle	heart
49	chr3:50610200-50618000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:50610200-50618800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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