Variant report

Variant	rs201193
Chromosome Location	chr3:50643305-50643306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50625312..50628212-chr3:50642289..50643959,2	K562	blood:
2	chr3:50643169..50645123-chr3:50685747..50687888,2	MCF-7	breast:
3	chr3:50599337..50613537-chr3:50634306..50660129,118	MCF-7	breast:
4	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:
5	chr3:50641854..50644392-chr3:51427006..51429676,2	MCF-7	breast:
6	chr3:50608161..50609853-chr3:50642051..50643670,2	K562	blood:

Variant related genes	Relation type
ENSG00000088543	Chromatin interaction
ENSG00000114735	Chromatin interaction
ENSG00000179837	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1013233	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1034405	0.86[EUR][1000 genomes]
rs11716398	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11719998	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12491425	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12493985	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs129310	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13076850	0.84[EUR][1000 genomes]
rs13083004	0.84[EUR][1000 genomes]
rs13091933	0.81[EUR][1000 genomes]
rs13094336	0.85[EUR][1000 genomes]
rs1385025	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1563684	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs175634	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17787569	0.85[EUR][1000 genomes]
rs1824281	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1966921	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1971976	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs201194	0.89[EUR][1000 genomes]
rs201196	0.86[EUR][1000 genomes]
rs201198	0.86[EUR][1000 genomes]
rs2086827	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2227280	0.85[EUR][1000 genomes]
rs2232248	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2232253	0.85[EUR][1000 genomes]
rs2269505	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269507	0.85[EUR][1000 genomes]
rs2355321	0.85[EUR][1000 genomes]
rs2355323	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34202063	0.85[EUR][1000 genomes]
rs34399912	0.85[EUR][1000 genomes]
rs34584636	0.85[EUR][1000 genomes]
rs34848480	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34889917	0.85[EUR][1000 genomes]
rs35655236	0.84[EUR][1000 genomes]
rs35690191	0.84[EUR][1000 genomes]
rs35714264	0.81[EUR][1000 genomes]
rs375544	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3792325	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3792328	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3804627	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3804632	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs391620	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3943212	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs396302	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs398703	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs399484	0.82[EUR][1000 genomes]
rs399971	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs414171	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs417592	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs441516	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs443030	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs443436	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs448028	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs453570	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688712	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs490634	0.87[EUR][1000 genomes]
rs59949730	0.85[EUR][1000 genomes]
rs616589	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs616689	0.84[AFR][1000 genomes]
rs622502	0.81[EUR][1000 genomes]
rs628081	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6446212	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6446213	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs67588094	0.85[EUR][1000 genomes]
rs6776224	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6778680	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6779819	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs67813889	0.87[EUR][1000 genomes]
rs6784166	0.81[EUR][1000 genomes]
rs6787521	0.84[EUR][1000 genomes]
rs6796769	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs695170	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71326937	0.85[EUR][1000 genomes]
rs728901	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs750453	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs750510	0.84[EUR][1000 genomes]
rs751851	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7615703	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7635666	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7645212	0.82[AMR][1000 genomes]
rs7646236	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs808149	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs809451	0.81[EUR][1000 genomes]
rs809454	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs813243	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs900735	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9682401	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9826757	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9868889	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50636600-50643600	Enhancers	Left Ventricle	heart
2	chr3:50636800-50646000	Genic enhancers	Fetal Intestine Small	intestine
3	chr3:50638800-50647400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:50639000-50643600	Weak transcription	Aorta	Aorta
5	chr3:50639000-50643800	Weak transcription	Brain Germinal Matrix	brain
6	chr3:50639000-50648000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:50639400-50648000	Weak transcription	Fetal Brain Female	brain
8	chr3:50639600-50646800	Genic enhancers	Spleen	Spleen
9	chr3:50639600-50648000	Weak transcription	Fetal Brain Male	brain
10	chr3:50639800-50644200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:50639800-50644800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:50639800-50648000	Weak transcription	HUVEC	blood vessel
13	chr3:50639800-50648200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:50639800-50648200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:50639800-50648200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:50640000-50644200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:50640000-50644600	Weak transcription	Thymus	Thymus
18	chr3:50640000-50647000	Genic enhancers	Fetal Muscle Leg	muscle
19	chr3:50640000-50648000	Weak transcription	Brain Substantia Nigra	brain
20	chr3:50640000-50648200	Weak transcription	NH-A	brain
21	chr3:50640200-50643800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:50640200-50644200	Weak transcription	NHLF	lung
23	chr3:50640200-50646200	Enhancers	Fetal Heart	heart
24	chr3:50640200-50647600	Weak transcription	Brain Anterior Caudate	brain
25	chr3:50640200-50647600	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr3:50640400-50643600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:50640400-50643800	Genic enhancers	Placenta	Placenta
28	chr3:50640400-50644200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:50640400-50646200	Genic enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:50640400-50646200	Genic enhancers	Fetal Intestine Large	intestine
31	chr3:50640400-50647200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:50640400-50648200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:50640400-50648200	Weak transcription	Osteobl	bone
34	chr3:50640600-50644000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:50640600-50644600	Strong transcription	Fetal Stomach	stomach
36	chr3:50640600-50646000	Genic enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:50640600-50649200	Transcr. at gene 5' and 3'	Dnd41	blood
38	chr3:50640800-50643400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:50640800-50643800	Enhancers	Ovary	ovary
40	chr3:50640800-50646200	Weak transcription	Fetal Kidney	kidney
41	chr3:50641200-50644600	Weak transcription	HMEC	breast
42	chr3:50641200-50645800	Strong transcription	Fetal Lung	lung
43	chr3:50641200-50646600	Genic enhancers	Lung	lung
44	chr3:50641200-50647000	Weak transcription	Small Intestine	intestine
45	chr3:50641400-50643400	Genic enhancers	Liver	Liver
46	chr3:50641400-50643400	Genic enhancers	Fetal Thymus	thymus
47	chr3:50641400-50643600	Genic enhancers	Rectal Mucosa Donor 31	rectum
48	chr3:50641400-50644000	Genic enhancers	Right Ventricle	heart
49	chr3:50641400-50646400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:50641600-50643800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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