Variant report

Variant	rs9645819
Chromosome Location	chr12:58270063-58270064
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58259629..58265686-chr12:58266089..58272179,8	K562	blood:
2	chr12:58262380..58265069-chr12:58266414..58270393,4	K562	blood:
3	chr12:58269021..58271713-chr12:58278735..58281292,2	MCF-7	breast:
4	chr12:58268216..58270366-chr12:58282645..58284163,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10431552	0.82[JPT][hapmap]
rs10444569	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10747783	0.83[JPT][hapmap]
rs10747784	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10747786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10747787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783847	0.82[JPT][hapmap]
rs10783848	0.81[JPT][hapmap]
rs10783850	0.87[JPT][hapmap]
rs10783851	0.86[JPT][hapmap]
rs10783854	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10783855	0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10783856	0.80[CEU][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10877012	0.82[JPT][hapmap]
rs10877014	0.82[JPT][hapmap]
rs10877015	0.82[JPT][hapmap]
rs10877016	0.82[JPT][hapmap]
rs10877019	0.82[JPT][hapmap]
rs10877028	0.87[JPT][hapmap]
rs10877029	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877030	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877031	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877032	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172333	0.82[JPT][hapmap]
rs11172335	0.82[JPT][hapmap]
rs11172343	0.83[JPT][hapmap]
rs11172344	0.82[JPT][hapmap]
rs11172349	0.82[JPT][hapmap]
rs11172351	0.82[JPT][hapmap]
rs11172361	0.81[AMR][1000 genomes]
rs11172367	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172368	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172371	0.82[CHB][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172378	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs12312955	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12319233	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12426201	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1599750	0.81[JPT][hapmap];0.86[AMR][1000 genomes]
rs1599751	0.87[JPT][hapmap];0.86[AMR][1000 genomes]
rs1599931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1875124	0.82[JPT][hapmap]
rs1875125	0.94[JPT][hapmap]
rs1962047	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2002275	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3751331	0.81[ASN][1000 genomes]
rs3825079	0.82[JPT][hapmap]
rs4237844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4646536	0.82[JPT][hapmap]
rs4760171	0.86[JPT][hapmap]
rs4760172	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760332	0.93[JPT][hapmap]
rs4760335	0.80[AMR][1000 genomes]
rs4760339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760340	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs4760341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs5017863	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59401446	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581155	0.82[JPT][hapmap]
rs6581157	0.82[ASN][1000 genomes]
rs703842	0.82[JPT][hapmap]
rs7134797	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724834	0.83[JPT][hapmap]
rs7312623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7489290	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs7969844	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181644	0.82[JPT][hapmap]
rs870392	0.93[JPT][hapmap]
rs871871	0.93[JPT][hapmap]
rs923829	0.83[JPT][hapmap]

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	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription 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	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9645819	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs9645819	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs9645819	XRCC6BP1	cis	Artery Aorta	GTEx
rs9645819	XRCC6BP1	cis	lung	GTEx
rs9645819	FAM119B	cis	Lymphoblastoid	GTEx
rs9645819	XRCC6BP1	cis	Artery Tibial	GTEx
rs9645819	XRCC6BP1	cis	Whole Blood	GTEx
rs9645819	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs9645819	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs9645819	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs9645819	XRCC6BP1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58263200-58271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:58263600-58275000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:58268400-58275000	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:58268800-58270200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:58268800-58270600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr12:58268800-58275200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:58268800-58275600	Weak transcription	Stomach Mucosa	stomach
8	chr12:58269400-58270200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:58269400-58270200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr12:58269400-58270200	Enhancers	GM12878-XiMat	blood
11	chr12:58269400-58270400	Enhancers	Psoas Muscle	Psoas
12	chr12:58269400-58270400	Enhancers	Right Atrium	heart
13	chr12:58269400-58270600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:58269600-58270200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:58269600-58270200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:58269600-58270200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr12:58269600-58270200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr12:58269600-58270200	Flanking Active TSS	NHLF	lung
19	chr12:58269600-58270400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:58269600-58270400	Enhancers	Aorta	Aorta
21	chr12:58269600-58270400	Enhancers	Colon Smooth Muscle	Colon
22	chr12:58269600-58270400	Flanking Active TSS	Osteobl	bone
23	chr12:58269800-58270400	Enhancers	Liver	Liver
24	chr12:58269800-58270400	Enhancers	Left Ventricle	heart
25	chr12:58269800-58270400	Enhancers	Lung	lung
26	chr12:58269800-58270400	Enhancers	Right Ventricle	heart
27	chr12:58270000-58270200	Enhancers	Placenta	Placenta
28	chr12:58270000-58270200	Enhancers	Fetal Stomach	stomach
29	chr12:58270000-58270400	Enhancers	Colonic Mucosa	Colon
30	chr12:58270000-58275200	Weak transcription	NHDF-Ad	bronchial
31	chr12:58270000-58275400	Weak transcription	K562	blood
32	chr12:58270000-58276200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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