Variant report

Variant	rs12260555
Chromosome Location	chr10:50026609-50026610
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:50025269-50027095	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50011032..50014812-chr10:50025927..50027937,3	K562	blood:
2	chr10:50023366..50027045-chr10:50027536..50030400,3	K562	blood:

Variant related genes	Relation type
WDFY4	TF binding region
ENSG00000128815	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10857653	0.97[ASN][1000 genomes]
rs11101512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11101515	0.94[ASN][1000 genomes]
rs11101516	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101518	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11101519	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11101520	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11101521	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11101522	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11101524	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11101525	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11101526	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11101527	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11101528	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12246033	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12247830	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12247839	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12248218	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12249974	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12251517	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12261146	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12264889	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12268007	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12268803	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17699445	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs17699451	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17836512	0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2377655	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2928402	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs2928403	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs3750864	0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs3789322	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs41283275	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs45520233	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4596990	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838883	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838884	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838885	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537578	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6537579	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7918931	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831865	chr10:49994254-50164239	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50005200-50026800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:50009600-50028000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:50013600-50028200	Strong transcription	Primary B cells from peripheral blood	blood
4	chr10:50013600-50061000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr10:50014200-50030000	Weak transcription	Right Atrium	heart
6	chr10:50015200-50063400	Strong transcription	Primary B cells from cord blood	blood
7	chr10:50015600-50029800	Weak transcription	Gastric	stomach
8	chr10:50016200-50063000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr10:50016200-50063000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr10:50016600-50062400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:50019400-50029000	Weak transcription	Primary T cells from cord blood	blood
12	chr10:50020000-50052000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr10:50021200-50027800	Weak transcription	Fetal Thymus	thymus
14	chr10:50022600-50040400	Weak transcription	Lung	lung
15	chr10:50023400-50029200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:50025000-50026800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr10:50025000-50062800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:50025200-50028600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr10:50025200-50028600	Strong transcription	Spleen	Spleen
20	chr10:50025200-50032000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr10:50025400-50029800	Weak transcription	Esophagus	oesophagus
22	chr10:50026000-50048200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr10:50026400-50027800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr10:50026600-50029400	Weak transcription	GM12878-XiMat	blood

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