Variant report

Variant	rs201196
Chromosome Location	chr3:50637070-50637071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50626963..50632967-chr3:50633102..50640850,17	K562	blood:
2	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
3	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:
4	chr3:50382035..50386464-chr3:50636911..50639420,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114388	Chromatin interaction
ENSG00000004838	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000114735	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1034405	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130252	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11710858	0.82[AMR][1000 genomes]
rs11719998	0.85[EUR][1000 genomes]
rs12491425	0.86[EUR][1000 genomes]
rs129310	0.90[EUR][1000 genomes]
rs13076850	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13083004	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084476	0.93[EUR][1000 genomes]
rs13091933	0.94[EUR][1000 genomes]
rs13094336	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094785	0.86[AMR][1000 genomes]
rs175634	0.89[EUR][1000 genomes]
rs17787569	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs201193	0.86[EUR][1000 genomes]
rs201194	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs201197	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227280	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232248	0.90[EUR][1000 genomes]
rs2232253	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269505	0.86[EUR][1000 genomes]
rs2269507	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355321	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355323	0.91[EUR][1000 genomes]
rs34202063	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34267788	0.89[EUR][1000 genomes]
rs34399912	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34434811	0.89[EUR][1000 genomes]
rs34584636	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34756253	0.93[EUR][1000 genomes]
rs34889917	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35655236	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35690191	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35714264	0.94[EUR][1000 genomes]
rs35864641	0.89[EUR][1000 genomes]
rs3804627	0.91[EUR][1000 genomes]
rs391620	0.85[EUR][1000 genomes]
rs398703	0.86[EUR][1000 genomes]
rs399484	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399971	0.89[EUR][1000 genomes]
rs414171	0.81[EUR][1000 genomes]
rs417592	0.91[EUR][1000 genomes]
rs441516	0.91[EUR][1000 genomes]
rs443030	0.90[EUR][1000 genomes]
rs4533647	0.89[EUR][1000 genomes]
rs453570	0.91[EUR][1000 genomes]
rs490634	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59949730	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622502	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs628081	0.83[EUR][1000 genomes]
rs6446210	0.82[AMR][1000 genomes]
rs67425923	0.84[EUR][1000 genomes]
rs67588094	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768300	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67813889	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784166	0.94[EUR][1000 genomes]
rs6787521	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs695170	0.91[EUR][1000 genomes]
rs71326937	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73082948	0.87[EUR][1000 genomes]
rs750453	0.85[EUR][1000 genomes]
rs7611428	0.82[AMR][1000 genomes]
rs7646236	0.91[EUR][1000 genomes]
rs7652260	0.82[EUR][1000 genomes]
rs809451	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs809454	0.87[EUR][1000 genomes]
rs9830920	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
11	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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
2	chr3:50628600-50638200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:50628800-50637200	Weak transcription	A549	lung
4	chr3:50628800-50637400	Weak transcription	Brain Substantia Nigra	brain
5	chr3:50629000-50637600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:50630400-50637200	Weak transcription	NHDF-Ad	bronchial
7	chr3:50630600-50637200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:50630600-50637400	Weak transcription	Stomach Mucosa	stomach
9	chr3:50632200-50637400	Weak transcription	Psoas Muscle	Psoas
10	chr3:50635200-50637400	Enhancers	Dnd41	blood
11	chr3:50635400-50637400	Enhancers	K562	blood
12	chr3:50635400-50637800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:50635600-50638800	Enhancers	Colon Smooth Muscle	Colon
14	chr3:50635800-50637600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:50635800-50638000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:50635800-50638200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:50635800-50638200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:50635800-50638200	Enhancers	HepG2	liver
19	chr3:50635800-50638600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:50635800-50640400	Enhancers	Placenta	Placenta
21	chr3:50636000-50637600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr3:50636000-50638000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr3:50636000-50638200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:50636000-50638400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:50636000-50638600	Enhancers	Primary T cells fromperipheralblood	blood
26	chr3:50636000-50638800	Enhancers	Right Ventricle	heart
27	chr3:50636000-50641200	Enhancers	Lung	lung
28	chr3:50636000-50641400	Enhancers	Fetal Thymus	thymus
29	chr3:50636000-50641600	Enhancers	Esophagus	oesophagus
30	chr3:50636200-50637200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:50636200-50638800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:50636200-50639000	Enhancers	Liver	Liver
33	chr3:50636200-50640600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:50636400-50637400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr3:50636400-50637600	Enhancers	Fetal Heart	heart
36	chr3:50636400-50638800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr3:50636400-50640600	Enhancers	Right Atrium	heart
38	chr3:50636400-50641000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:50636400-50641600	Enhancers	Pancreas	Pancrea
40	chr3:50636600-50637600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:50636600-50637600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:50636600-50637600	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr3:50636600-50638000	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr3:50636600-50638400	Enhancers	Ovary	ovary
45	chr3:50636600-50638400	Enhancers	HSMMtube	muscle
46	chr3:50636600-50638800	Enhancers	Fetal Intestine Large	intestine
47	chr3:50636600-50638800	Enhancers	Fetal Muscle Trunk	muscle
48	chr3:50636600-50639000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr3:50636600-50639200	Enhancers	Fetal Muscle Leg	muscle
50	chr3:50636600-50639600	Enhancers	Spleen	Spleen

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