Variant report

Variant	rs441516
Chromosome Location	chr3:50628931-50628932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50619029..50623920-chr3:50628439..50631863,6	MCF-7	breast:
2	chr3:50604804..50606587-chr3:50626541..50629507,2	K562	blood:
3	chr3:50626963..50632967-chr3:50633102..50640850,17	K562	blood:
4	chr3:50628346..50630118-chr3:50630159..50631667,2	K562	blood:
5	chr3:50373283..50375179-chr3:50628099..50629675,2	K562	blood:
6	chr3:50624179..50629741-chr3:50646689..50652947,9	K562	blood:

Variant related genes	Relation type
ENSG00000114735	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000088543	Chromatin interaction
ENSG00000114737	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1013233	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1034405	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs11130252	0.84[EUR][1000 genomes]
rs11712367	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11716398	0.87[AMR][1000 genomes]
rs11719998	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491425	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12493985	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12639126	0.81[CEU][hapmap]
rs129310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13076850	0.89[EUR][1000 genomes]
rs13083004	0.89[EUR][1000 genomes]
rs13084476	0.84[EUR][1000 genomes]
rs13091933	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs13094336	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1385025	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs175634	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17787569	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1824281	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1971976	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs201193	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs201194	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs201196	0.91[EUR][1000 genomes]
rs201197	0.80[EUR][1000 genomes]
rs201198	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2227280	0.90[EUR][1000 genomes]
rs2232248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232253	0.90[EUR][1000 genomes]
rs2269505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269507	0.90[EUR][1000 genomes]
rs2355321	0.90[EUR][1000 genomes]
rs2355323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2675773	0.88[CEU][hapmap]
rs2675816	0.83[CEU][hapmap]
rs34202063	0.90[EUR][1000 genomes]
rs34267788	0.81[EUR][1000 genomes]
rs34399912	0.90[EUR][1000 genomes]
rs34434811	0.81[EUR][1000 genomes]
rs34584636	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs34756253	0.84[EUR][1000 genomes]
rs34848480	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34889917	0.90[EUR][1000 genomes]
rs35655236	0.89[EUR][1000 genomes]
rs35690191	0.89[EUR][1000 genomes]
rs35714264	0.85[EUR][1000 genomes]
rs35864641	0.81[EUR][1000 genomes]
rs375544	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3792323	0.82[CHB][hapmap]
rs3792325	0.90[CHB][hapmap];0.90[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3792328	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3804627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3804632	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs388483	0.93[YRI][hapmap]
rs391620	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3943212	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs396302	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs398703	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs399484	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs399971	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414171	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs417592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs443030	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs443436	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs448028	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4485709	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4533647	0.81[EUR][1000 genomes]
rs453570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688712	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs490634	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs59949730	0.90[EUR][1000 genomes]
rs616589	0.90[CHB][hapmap];0.81[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs622502	0.81[EUR][1000 genomes]
rs628081	0.94[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6446212	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6446213	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs6446220	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs67588094	0.90[EUR][1000 genomes]
rs6778680	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs6779819	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes]
rs67813889	0.92[EUR][1000 genomes]
rs6784166	0.85[EUR][1000 genomes]
rs6787521	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6796769	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs695170	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71326937	0.90[EUR][1000 genomes]
rs728901	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs750453	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs750510	0.89[CEU][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs751851	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs754298	0.82[EUR][1000 genomes]
rs7615703	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7635666	0.87[AMR][1000 genomes]
rs7645212	0.80[AMR][1000 genomes]
rs7646236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs808149	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs809451	0.81[EUR][1000 genomes]
rs809454	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs813243	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs900735	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9682401	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9825535	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs9826757	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9830920	0.82[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:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
2	chr3:50622400-50629800	Weak transcription	Fetal Lung	lung
3	chr3:50623000-50636600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:50623200-50633800	Enhancers	Fetal Thymus	thymus
5	chr3:50624400-50629600	Weak transcription	Fetal Stomach	stomach
6	chr3:50625200-50630600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:50626400-50629600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:50626800-50629400	Enhancers	HepG2	liver
9	chr3:50626800-50632400	Enhancers	Liver	Liver
10	chr3:50627200-50629800	Weak transcription	Fetal Intestine Small	intestine
11	chr3:50627800-50629000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr3:50627800-50630000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr3:50628000-50629000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:50628000-50629000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr3:50628000-50629000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr3:50628000-50629000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:50628000-50629000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr3:50628000-50629000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr3:50628000-50629200	Flanking Active TSS	Dnd41	blood
20	chr3:50628000-50629200	Flanking Active TSS	K562	blood
21	chr3:50628000-50629400	Enhancers	Psoas Muscle	Psoas
22	chr3:50628000-50629400	Enhancers	Right Atrium	heart
23	chr3:50628000-50629400	Enhancers	Right Ventricle	heart
24	chr3:50628000-50630000	Enhancers	Osteobl	bone
25	chr3:50628000-50630400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:50628000-50630600	Enhancers	Stomach Mucosa	stomach
27	chr3:50628000-50630600	Enhancers	Spleen	Spleen
28	chr3:50628000-50630800	Enhancers	Esophagus	oesophagus
29	chr3:50628000-50630800	Enhancers	Fetal Muscle Trunk	muscle
30	chr3:50628000-50630800	Enhancers	Gastric	stomach
31	chr3:50628000-50630800	Enhancers	Pancreas	Pancrea
32	chr3:50628000-50630800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:50628000-50630800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr3:50628000-50631000	Enhancers	Fetal Muscle Leg	muscle
35	chr3:50628000-50631200	Enhancers	Placenta	Placenta
36	chr3:50628000-50631200	Enhancers	Left Ventricle	heart
37	chr3:50628000-50631200	Enhancers	Lung	lung
38	chr3:50628200-50629000	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr3:50628200-50629000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:50628200-50629000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:50628200-50629200	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr3:50628200-50629400	Enhancers	Colonic Mucosa	Colon
43	chr3:50628200-50630400	Enhancers	Small Intestine	intestine
44	chr3:50628200-50632400	Enhancers	Fetal Heart	heart
45	chr3:50628400-50629000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:50628400-50629400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:50628400-50630600	Enhancers	Primary B cells from peripheral blood	blood
48	chr3:50628400-50630800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:50628400-50632000	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr3:50628400-50633800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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