Variant report

Variant	rs2285090
Chromosome Location	chr3:50620043-50620044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:
2	chr3:50614914..50616953-chr3:50617610..50620432,2	MCF-7	breast:
3	chr3:50619029..50623920-chr3:50628439..50631863,6	MCF-7	breast:
4	chr3:50378822..50381164-chr3:50619483..50621756,2	K562	blood:
5	chr3:50607065..50611118-chr3:50617412..50623416,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088543	Chromatin interaction
ENSG00000004838	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000114737	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1077215	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs1107312	0.85[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12486143	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486717	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12487817	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12489607	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12491440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12491812	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12492093	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12492540	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12492982	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12494094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12494326	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494707	0.81[AMR][1000 genomes]
rs12495399	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs17050991	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17050995	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17051000	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17051043	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17051045	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17051403	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs175634	0.81[CHD][hapmap]
rs1872184	0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1894459	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035484	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs2076927	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2170840	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs2227292	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2227293	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239750	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2239751	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2239752	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239753	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749265	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3752449	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3792323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3806706	0.85[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4476497	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4640555	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4688696	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs4688705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4688707	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688709	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4688710	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688713	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4688715	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4688716	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56170012	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56856095	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57910827	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58427389	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58529408	0.80[ASN][1000 genomes]
rs59036236	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60552073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60877431	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61193866	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61316441	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61574029	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61613532	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs616689	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6446208	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs650655	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6766638	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6771348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6783922	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6794155	0.85[ASN][1000 genomes]
rs728902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72938758	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72942785	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72942794	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72944726	0.80[ASN][1000 genomes]
rs72944730	0.80[ASN][1000 genomes]
rs73835531	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs743753	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs745356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs762889	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs808148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs876103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs876104	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs876105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9814874	0.85[CHB][hapmap]
rs9868889	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9879397	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50607400-50628200	Weak transcription	Small Intestine	intestine
2	chr3:50607600-50628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:50607800-50628200	Weak transcription	HSMMtube	muscle
4	chr3:50607800-50628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:50608000-50621400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:50608000-50621400	Weak transcription	HUVEC	blood vessel
7	chr3:50608000-50621800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:50608200-50624000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:50608200-50628400	Weak transcription	A549	lung
10	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
11	chr3:50608400-50625600	Weak transcription	NHDF-Ad	bronchial
12	chr3:50609200-50620800	Strong transcription	Brain Germinal Matrix	brain
13	chr3:50609800-50620600	Strong transcription	Fetal Brain Female	brain
14	chr3:50610000-50621400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:50610000-50623000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:50610200-50620400	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr3:50610200-50623600	Strong transcription	Fetal Muscle Leg	muscle
18	chr3:50610200-50624400	Strong transcription	Fetal Stomach	stomach
19	chr3:50610200-50628000	Weak transcription	Stomach Mucosa	stomach
20	chr3:50610400-50622400	Weak transcription	GM12878-XiMat	blood
21	chr3:50610400-50623200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:50610400-50623200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr3:50610400-50628400	Weak transcription	HSMM	muscle
24	chr3:50610600-50627600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:50611000-50620600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:50611200-50621600	Strong transcription	Thymus	Thymus
27	chr3:50611400-50621600	Strong transcription	Fetal Intestine Small	intestine
28	chr3:50612200-50621400	Strong transcription	Fetal Intestine Large	intestine
29	chr3:50612400-50620600	Strong transcription	Spleen	Spleen
30	chr3:50613000-50620600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr3:50613000-50622400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:50613400-50620400	Strong transcription	Gastric	stomach
33	chr3:50613400-50621200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:50613400-50628000	Weak transcription	HMEC	breast
35	chr3:50613600-50621400	Strong transcription	Esophagus	oesophagus
36	chr3:50613800-50621200	Strong transcription	Brain Substantia Nigra	brain
37	chr3:50614000-50620200	Strong transcription	Brain Hippocampus Middle	brain
38	chr3:50614200-50620200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:50614200-50620200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr3:50614200-50620400	Strong transcription	Brain Anterior Caudate	brain
41	chr3:50614400-50620400	Strong transcription	Colonic Mucosa	Colon
42	chr3:50614400-50620600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:50614400-50621800	Strong transcription	Dnd41	blood
44	chr3:50614600-50621800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:50614800-50620400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:50614800-50620800	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:50615600-50620200	Weak transcription	Aorta	Aorta
48	chr3:50615600-50621000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:50615800-50621800	Weak transcription	K562	blood
50	chr3:50616000-50620600	Strong transcription	Fetal Thymus	thymus

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