Variant report

Variant	rs9881008
Chromosome Location	chr3:50047404-50047405
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	chr3:50035315..50037436-chr3:50045585..50047929,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11130226	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11130228	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11130229	0.86[EUR][1000 genomes]
rs11130233	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11130234	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11713562	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11925192	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12485600	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12496973	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13060128	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2240329	0.81[EUR][1000 genomes]
rs2245365	0.83[EUR][1000 genomes]
rs2252833	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2353579	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2353586	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353587	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526748	0.84[EUR][1000 genomes]
rs2526751	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2624843	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2624844	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2681778	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2883057	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34080578	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35065728	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3774733	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4688689	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4688690	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4688755	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4688756	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4688757	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4688758	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55751738	0.90[EUR][1000 genomes]
rs6446189	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6446190	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446193	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66851636	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6765484	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6767381	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6771546	0.89[EUR][1000 genomes]
rs6772095	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6780731	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6792892	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72942333	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7609971	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7613875	0.85[EUR][1000 genomes]
rs7621026	0.91[EUR][1000 genomes]
rs7621352	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7628058	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7634917	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7635002	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7650214	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9311446	0.84[EUR][1000 genomes]
rs9810125	0.83[EUR][1000 genomes]
rs9814664	0.85[EUR][1000 genomes]
rs9853222	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9861216	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9866695	0.87[AMR][1000 genomes];0.90[EUR][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
rs9881008	RBM6	cis	lung	GTEx
rs9881008	RBM6	cis	Whole Blood	GTEx
rs9881008	RBM6	cis	Heart Left Ventricle	GTEx
rs9881008	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs9881008	RBM6	cis	Artery Tibial	GTEx
rs9881008	RBM6	cis	Artery Aorta	GTEx
rs9881008	RBM6	cis	Esophagus Mucosa	GTEx
rs9881008	RBM6	cis	Thyroid	GTEx
rs9881008	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9881008	RBM6	cis	Stomach	GTEx
rs9881008	RBM6	cis	Adipose Subcutaneous	GTEx
rs9881008	RBM6	cis	Esophagus Muscularis	GTEx
rs9881008	RBM6	cis	Nerve Tibial	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	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
6	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:50010800-50087000	Weak transcription	NHLF	lung
8	chr3:50011000-50048400	Weak transcription	A549	lung
9	chr3:50011000-50051000	Weak transcription	Pancreas	Pancrea
10	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
12	chr3:50012400-50049000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:50028000-50056400	Weak transcription	Ovary	ovary
15	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
16	chr3:50029800-50050800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
18	chr3:50031000-50048000	Strong transcription	Fetal Thymus	thymus
19	chr3:50033800-50051000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:50035200-50058200	Weak transcription	Esophagus	oesophagus
21	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
22	chr3:50036800-50048000	Strong transcription	Fetal Stomach	stomach
23	chr3:50036800-50054600	Strong transcription	Fetal Intestine Small	intestine
24	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:50037600-50049200	Weak transcription	Brain Germinal Matrix	brain
26	chr3:50037600-50055400	Weak transcription	Hela-S3	cervix
27	chr3:50037600-50061800	Weak transcription	Small Intestine	intestine
28	chr3:50038400-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:50038800-50056800	Weak transcription	HepG2	liver
31	chr3:50039400-50050200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:50039400-50061800	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:50039400-50084600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:50039600-50050400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:50040400-50056000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:50041000-50047800	Strong transcription	Primary T cells from cord blood	blood
37	chr3:50041200-50051600	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:50041400-50053400	Weak transcription	Fetal Lung	lung
39	chr3:50041400-50057000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:50041600-50050400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr3:50041600-50051000	Weak transcription	Brain Anterior Caudate	brain
43	chr3:50041600-50053400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:50041600-50055200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:50041600-50056800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:50041600-50057000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:50041600-50058200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:50041600-50061600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:50041600-50063000	Weak transcription	Brain Substantia Nigra	brain
50	chr3:50041600-50065200	Weak transcription	NH-A	brain

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