Variant report

Variant	rs13063621
Chromosome Location	chr3:49821625-49821626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49737567..49739735-chr3:49821150..49823977,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164068	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10049413	0.88[ASN][1000 genomes]
rs1049256	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10865958	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865959	0.88[ASN][1000 genomes]
rs11130214	0.92[ASN][1000 genomes]
rs11130216	0.92[ASN][1000 genomes]
rs11130218	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130219	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130221	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128535	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11709680	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11710675	0.94[ASN][1000 genomes]
rs11714957	0.96[ASN][1000 genomes]
rs11715304	0.91[ASN][1000 genomes]
rs11716575	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11717256	0.92[ASN][1000 genomes]
rs11717463	0.96[ASN][1000 genomes]
rs11920900	0.95[ASN][1000 genomes]
rs12381242	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12490656	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12496226	0.87[ASN][1000 genomes]
rs13084243	0.96[ASN][1000 genomes]
rs13085679	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13086130	0.96[ASN][1000 genomes]
rs13086465	0.94[ASN][1000 genomes]
rs13090611	0.88[ASN][1000 genomes]
rs1317140	0.83[ASN][1000 genomes]
rs13316065	0.87[ASN][1000 genomes]
rs1491986	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1799843	0.89[ASN][1000 genomes]
rs1799845	0.89[ASN][1000 genomes]
rs2234385	0.89[ASN][1000 genomes]
rs2234391	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2246832	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2247036	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271960	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271961	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276864	0.88[ASN][1000 genomes]
rs2291542	0.94[ASN][1000 genomes]
rs2307021	0.94[ASN][1000 genomes]
rs2352967	0.87[ASN][1000 genomes]
rs2352974	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2352975	0.88[ASN][1000 genomes]
rs34451146	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34522271	0.96[ASN][1000 genomes]
rs34614773	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34735338	0.94[ASN][1000 genomes]
rs35210174	0.96[ASN][1000 genomes]
rs35261599	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35474403	0.96[ASN][1000 genomes]
rs3749237	0.96[ASN][1000 genomes]
rs3749240	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749241	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811695	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3811696	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3819325	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4519692	0.83[ASN][1000 genomes]
rs4768	0.94[ASN][1000 genomes]
rs4855841	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4855850	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4855862	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4855867	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57648519	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59906301	0.92[ASN][1000 genomes]
rs60205400	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260715	0.94[ASN][1000 genomes]
rs62260719	0.89[ASN][1000 genomes]
rs62260729	0.88[ASN][1000 genomes]
rs6446295	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766836	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775384	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6785549	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802890	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804655	0.92[ASN][1000 genomes]
rs695238	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71324996	0.80[ASN][1000 genomes]
rs7372725	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7372730	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7372966	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7374183	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7374277	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7426497	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7429353	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7431078	0.96[ASN][1000 genomes]
rs7431106	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618501	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618519	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7629936	0.88[ASN][1000 genomes]
rs7634886	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7634902	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645061	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7648987	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7649348	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814765	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815766	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819511	0.86[ASN][1000 genomes]
rs9850465	0.86[ASN][1000 genomes]
rs9853458	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9855505	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9859153	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865480	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9871654	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9872864	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9873183	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9876508	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9882639	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13063621	RBM6	cis	Nerve Tibial	GTEx
rs13063621	RBM6	cis	Artery Tibial	GTEx
rs13063621	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs13063621	RBM6	cis	lung	GTEx
rs13063621	RBM6	cis	Thyroid	GTEx
rs13063621	RBM6	cis	Esophagus Muscularis	GTEx
rs13063621	UBA7	cis	Whole Blood	GTEx
rs13063621	FAM212A	cis	Esophagus Mucosa	GTEx
rs13063621	RBM6	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:49785600-49822400	Weak transcription	HSMMtube	muscle
3	chr3:49785600-49822600	Weak transcription	Esophagus	oesophagus
4	chr3:49786000-49823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:49786200-49822400	Weak transcription	HMEC	breast
6	chr3:49795400-49822400	Weak transcription	Stomach Mucosa	stomach
7	chr3:49804000-49822600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:49807800-49822600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:49809400-49822800	Weak transcription	A549	lung
10	chr3:49809600-49822400	Weak transcription	NHDF-Ad	bronchial
11	chr3:49810400-49822400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49812000-49822800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:49812200-49822800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:49812800-49821800	Weak transcription	Fetal Heart	heart
15	chr3:49812800-49822400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:49812800-49822400	Weak transcription	HSMM	muscle
17	chr3:49813200-49822400	Weak transcription	Hela-S3	cervix
18	chr3:49814000-49821800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:49814800-49822400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:49815800-49822400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:49816600-49821800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:49816600-49822600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:49817400-49822000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:49817800-49822000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:49818200-49821800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr3:49818200-49822200	Strong transcription	Fetal Intestine Large	intestine
27	chr3:49818200-49823200	Weak transcription	Gastric	stomach
28	chr3:49818400-49821800	Strong transcription	Placenta	Placenta
29	chr3:49818400-49822200	Weak transcription	Psoas Muscle	Psoas
30	chr3:49818400-49822200	Strong transcription	Thymus	Thymus
31	chr3:49818400-49822400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:49818400-49822400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:49818600-49822400	Strong transcription	Fetal Intestine Small	intestine
34	chr3:49818600-49822400	Weak transcription	NH-A	brain
35	chr3:49818800-49821800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:49819200-49821800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:49819200-49821800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:49819200-49821800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:49819200-49821800	Strong transcription	Left Ventricle	heart
40	chr3:49819200-49822000	Weak transcription	Primary B cells from cord blood	blood
41	chr3:49819200-49822200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:49819200-49822400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:49819200-49822400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:49819200-49822400	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:49819200-49822400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:49819200-49822400	Weak transcription	Fetal Kidney	kidney
47	chr3:49819200-49822400	Strong transcription	Fetal Thymus	thymus
48	chr3:49819200-49822400	Weak transcription	Small Intestine	intestine
49	chr3:49819200-49822400	Weak transcription	Spleen	Spleen
50	chr3:49819200-49822600	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links