Variant report

Variant	rs13090611
Chromosome Location	chr3:49783946-49783947
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	chr3:49782178..49785035-chr3:49823443..49825758,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10049413	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1049256	0.88[ASN][1000 genomes]
rs10865958	0.83[ASN][1000 genomes]
rs10865959	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130214	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130216	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130218	0.86[ASN][1000 genomes]
rs11130219	0.86[ASN][1000 genomes]
rs11130221	0.88[ASN][1000 genomes]
rs1128535	0.83[ASN][1000 genomes]
rs11709680	0.86[ASN][1000 genomes]
rs11710675	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11714957	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715304	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11716575	0.86[ASN][1000 genomes]
rs11717256	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11717463	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11920900	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12381242	0.86[ASN][1000 genomes]
rs12490656	0.83[ASN][1000 genomes]
rs12496226	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13063621	0.88[ASN][1000 genomes]
rs13084243	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13085679	0.83[ASN][1000 genomes]
rs13086130	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13086465	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1317140	0.88[EUR][1000 genomes]
rs13316065	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1491986	0.86[ASN][1000 genomes]
rs1799843	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1799845	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2234385	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2234391	0.83[ASN][1000 genomes]
rs2246832	0.81[ASN][1000 genomes]
rs2247036	0.81[ASN][1000 genomes]
rs2271960	0.81[ASN][1000 genomes]
rs2271961	0.81[ASN][1000 genomes]
rs2276864	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2291542	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2307021	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2352967	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2352974	0.81[ASN][1000 genomes]
rs2352975	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34451146	0.88[ASN][1000 genomes]
rs34522271	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34614773	0.86[ASN][1000 genomes]
rs34735338	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35210174	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35261599	0.90[ASN][1000 genomes]
rs35474403	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3749237	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3749240	0.88[ASN][1000 genomes]
rs3749241	0.88[ASN][1000 genomes]
rs3811695	0.84[ASN][1000 genomes]
rs3811696	0.86[ASN][1000 genomes]
rs4768	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4855841	0.83[ASN][1000 genomes]
rs4855850	0.90[ASN][1000 genomes]
rs4855862	0.86[ASN][1000 genomes]
rs4855867	0.86[ASN][1000 genomes]
rs57648519	0.88[ASN][1000 genomes]
rs59906301	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60205400	0.88[ASN][1000 genomes]
rs62260715	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62260719	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62260729	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6446295	0.90[ASN][1000 genomes]
rs6766836	0.88[ASN][1000 genomes]
rs6775384	0.83[ASN][1000 genomes]
rs6785549	0.88[ASN][1000 genomes]
rs6802890	0.88[ASN][1000 genomes]
rs6804655	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs695238	0.83[ASN][1000 genomes]
rs71324996	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7372725	0.96[ASN][1000 genomes]
rs7372730	0.99[ASN][1000 genomes]
rs7372966	0.96[ASN][1000 genomes]
rs7374183	0.96[ASN][1000 genomes]
rs7374277	0.96[ASN][1000 genomes]
rs7429353	0.96[ASN][1000 genomes]
rs7431078	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7431106	0.88[ASN][1000 genomes]
rs7618501	0.89[ASN][1000 genomes]
rs7618519	0.90[ASN][1000 genomes]
rs7629936	0.85[ASN][1000 genomes]
rs7634886	0.86[ASN][1000 genomes]
rs7634902	0.88[ASN][1000 genomes]
rs7645061	0.83[ASN][1000 genomes]
rs7648987	0.83[ASN][1000 genomes]
rs7649348	0.90[ASN][1000 genomes]
rs9814765	0.86[ASN][1000 genomes]
rs9815766	0.88[ASN][1000 genomes]
rs9819511	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9850465	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9853458	0.90[ASN][1000 genomes]
rs9855505	0.96[ASN][1000 genomes]
rs9859153	0.88[ASN][1000 genomes]
rs9865480	0.90[ASN][1000 genomes]
rs9871654	0.87[ASN][1000 genomes]
rs9872864	0.96[ASN][1000 genomes]
rs9873183	0.86[ASN][1000 genomes]
rs9876508	0.90[ASN][1000 genomes]
rs9882639	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13090611	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs13090611	WDR6	cis	Whole Blood	GTEx
rs13090611	RBM6	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49762600-49785200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:49762600-49809000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:49763000-49784800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:49765800-49785800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:49767600-49787800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr3:49768200-49787600	Strong transcription	Primary B cells from peripheral blood	blood
7	chr3:49772600-49785400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:49772600-49791600	Weak transcription	Right Atrium	heart
9	chr3:49774000-49788200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:49775600-49788200	Weak transcription	Stomach Mucosa	stomach
11	chr3:49775600-49817000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:49775800-49810200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:49776000-49784000	Weak transcription	A549	lung
15	chr3:49776000-49784600	Weak transcription	Left Ventricle	heart
16	chr3:49776000-49785200	Weak transcription	GM12878-XiMat	blood
17	chr3:49776000-49789400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:49776000-49791200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:49776000-49791800	Weak transcription	Psoas Muscle	Psoas
20	chr3:49776200-49784200	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:49776200-49784800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:49776200-49784800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:49776200-49784800	Weak transcription	Aorta	Aorta
24	chr3:49776200-49784800	Weak transcription	Liver	Liver
25	chr3:49776200-49784800	Weak transcription	Brain Germinal Matrix	brain
26	chr3:49776200-49784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:49776200-49785200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:49776200-49785200	Weak transcription	Colonic Mucosa	Colon
29	chr3:49776200-49790400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:49776200-49799000	Weak transcription	Fetal Heart	heart
31	chr3:49776200-49802000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:49776400-49784000	Weak transcription	HepG2	liver
33	chr3:49776400-49784200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:49776400-49784200	Weak transcription	Fetal Brain Female	brain
35	chr3:49776400-49784800	Weak transcription	Brain Substantia Nigra	brain
36	chr3:49776400-49784800	Weak transcription	HMEC	breast
37	chr3:49776400-49785000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:49776400-49785000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:49776400-49785200	Weak transcription	Esophagus	oesophagus
40	chr3:49776400-49785200	Weak transcription	Pancreas	Pancrea
41	chr3:49776400-49785200	Weak transcription	Spleen	Spleen
42	chr3:49776400-49785800	Weak transcription	Fetal Lung	lung
43	chr3:49776400-49787400	Weak transcription	Fetal Brain Male	brain
44	chr3:49776400-49788600	Strong transcription	Fetal Thymus	thymus
45	chr3:49776400-49794400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr3:49776400-49797400	Weak transcription	Small Intestine	intestine
47	chr3:49776400-49812000	Weak transcription	HSMM	muscle
48	chr3:49776400-49812200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:49776400-49812600	Weak transcription	Gastric	stomach
50	chr3:49776400-49818000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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