Variant report

Variant	rs2353586
Chromosome Location	chr3:50046046-50046047
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50035315..50037436-chr3:50045585..50047929,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10049087	0.85[AMR][1000 genomes]
rs1062633	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11130224	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11130226	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130228	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130229	0.89[EUR][1000 genomes]
rs11130233	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130234	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11713193	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11713562	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11925192	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12485600	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12496973	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13060128	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1317154	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2230590	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2240326	0.83[AMR][1000 genomes]
rs2240327	0.84[AMR][1000 genomes]
rs2240329	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2245365	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2252833	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2280406	0.84[ASN][1000 genomes]
rs2353579	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2353587	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2526743	0.82[AMR][1000 genomes]
rs2526748	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526751	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2624816	0.82[AMR][1000 genomes]
rs2624823	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2624824	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2624825	0.80[EUR][1000 genomes]
rs2624843	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2624844	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2681778	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2681780	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2681781	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2856234	0.80[EUR][1000 genomes]
rs2883057	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34080578	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34831713	0.81[AMR][1000 genomes]
rs35065728	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3733133	0.80[EUR][1000 genomes]
rs3733135	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3774733	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3774758	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4688689	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4688690	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4688755	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4688756	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4688757	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4688758	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55751738	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62262093	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6446187	0.83[ASN][1000 genomes]
rs6446189	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6446190	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446193	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66851636	0.85[EUR][1000 genomes]
rs6765484	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6767381	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6771546	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6772095	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6780731	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792892	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6795703	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72942333	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7609971	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7613875	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7621026	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7621352	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7628058	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7634084	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7634917	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7635002	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7650214	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9311446	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9810125	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9814664	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9821675	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9843653	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9848497	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9853222	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9856572	0.81[AMR][1000 genomes]
rs9861216	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9862795	0.84[ASN][1000 genomes]
rs9866695	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9881008	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2353586	RBM6	cis	Esophagus Muscularis	GTEx
rs2353586	RBM6	cis	Whole Blood	GTEx
rs2353586	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2353586	RBM6	cis	Nerve Tibial	GTEx
rs2353586	RBM6	cis	Artery Tibial	GTEx
rs2353586	RBM6	cis	Artery Aorta	GTEx
rs2353586	RBM6	cis	Stomach	GTEx
rs2353586	RBM6	cis	lung	GTEx
rs2353586	RBM6	cis	Esophagus Mucosa	GTEx
rs2353586	RBM6	cis	Heart Left Ventricle	GTEx
rs2353586	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs2353586	RBM6	cis	Adipose Subcutaneous	GTEx
rs2353586	RBM6	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:49998400-50078600	Weak transcription	K562	blood
3	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50005200-50046400	Weak transcription	Psoas Muscle	Psoas
5	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
7	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:50010800-50087000	Weak transcription	NHLF	lung
9	chr3:50011000-50046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:50011000-50046400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:50011000-50048400	Weak transcription	A549	lung
12	chr3:50011000-50051000	Weak transcription	Pancreas	Pancrea
13	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
15	chr3:50012400-50049000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:50015400-50046400	Weak transcription	Fetal Kidney	kidney
18	chr3:50022200-50046400	Weak transcription	Gastric	stomach
19	chr3:50028000-50056400	Weak transcription	Ovary	ovary
20	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
21	chr3:50029800-50050800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
23	chr3:50031000-50048000	Strong transcription	Fetal Thymus	thymus
24	chr3:50033800-50051000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:50035200-50058200	Weak transcription	Esophagus	oesophagus
26	chr3:50035600-50047200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:50036400-50046800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
29	chr3:50036800-50048000	Strong transcription	Fetal Stomach	stomach
30	chr3:50036800-50054600	Strong transcription	Fetal Intestine Small	intestine
31	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr3:50037600-50046200	Weak transcription	NHEK	skin
33	chr3:50037600-50046400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:50037600-50046600	Weak transcription	Lung	lung
35	chr3:50037600-50049200	Weak transcription	Brain Germinal Matrix	brain
36	chr3:50037600-50055400	Weak transcription	Hela-S3	cervix
37	chr3:50037600-50061800	Weak transcription	Small Intestine	intestine
38	chr3:50037800-50046200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:50038400-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:50038800-50056800	Weak transcription	HepG2	liver
42	chr3:50039000-50046200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:50039000-50046400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:50039400-50046200	Weak transcription	HMEC	breast
45	chr3:50039400-50046400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:50039400-50050200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:50039400-50061800	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:50039400-50084600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:50039600-50046400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:50039600-50046400	Weak transcription	Duodenum Mucosa	Duodenum

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