Variant report

Variant	rs10169613
Chromosome Location	chr2:111934977-111934978
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	chr2:111933860..111937323-chr2:111941659..111944364,3	MCF-7	breast:
2	chr2:111923929..111929033-chr2:111931509..111935010,6	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10166773	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10189015	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10199020	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10211562	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10439381	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10439396	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054873	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs11123407	0.81[ASN][1000 genomes]
rs11674517	0.81[CEU][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11899831	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13398360	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1439287	0.86[JPT][hapmap]
rs1821968	0.86[JPT][hapmap]
rs1837366	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs1837367	0.86[JPT][hapmap]
rs1837369	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs2165107	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241842	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs28723045	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789061	0.81[CEU][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3789064	0.85[ASN][1000 genomes]
rs3789065	0.81[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3789068	0.81[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3898882	0.83[EUR][1000 genomes]
rs4627572	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs4848406	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4849402	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs55878194	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs586283	0.80[EUR][1000 genomes]
rs60982612	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6542350	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6708784	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6726007	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732491	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6734942	0.84[ASN][1000 genomes]
rs6754738	0.82[EUR][1000 genomes]
rs6755484	0.81[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs6760053	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs744530	0.90[MEX][hapmap]
rs7562480	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7565445	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7565457	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7565473	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7567184	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7569300	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572367	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7581735	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7585054	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7588534	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7596789	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879623	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9308742	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938095	0.85[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs9808225	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1803356	chr2:111899783-112662597	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv428402	chr2:111899783-112662597	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers 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 miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv520700	chr2:111931421-111948809	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10169613	BCL2L11	cis	cerebellum	SCAN
rs10169613	SULT1C2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111920800-111943000	Weak transcription	Right Ventricle	heart
2	chr2:111921200-111939400	Weak transcription	Right Atrium	heart
3	chr2:111929400-111942200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:111932200-111939200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:111932800-111937600	Enhancers	Liver	Liver
6	chr2:111933000-111938400	Enhancers	Pancreas	Pancrea
7	chr2:111933400-111936200	Enhancers	HepG2	liver
8	chr2:111933600-111945200	Enhancers	Fetal Intestine Small	intestine
9	chr2:111933800-111936200	Enhancers	A549	lung
10	chr2:111934000-111945000	Enhancers	Fetal Intestine Large	intestine
11	chr2:111934200-111935000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:111934800-111935000	Enhancers	Placenta	Placenta
13	chr2:111934800-111935000	Enhancers	Stomach Mucosa	stomach
14	chr2:111934800-111935800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:111934800-111935800	Weak transcription	Gastric	stomach
16	chr2:111934800-111936000	Weak transcription	Adipose Nuclei	Adipose
17	chr2:111934800-111936400	Weak transcription	Esophagus	oesophagus
18	chr2:111934800-111936400	Weak transcription	Left Ventricle	heart
19	chr2:111934800-111941800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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