Variant report

Variant	rs9308742
Chromosome Location	chr2:111943621-111943622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:111941236..111945109-chr2:111946384..111948613,3	K562	blood:
2	chr2:111943401..111945501-chr2:111991303..111993728,2	K562	blood:
3	chr2:111938737..111942201-chr2:111942427..111945208,3	K562	blood:
4	chr2:111941236..111945109-chr2:111946384..111948560,3	K562	blood:
5	chr2:111933860..111937323-chr2:111941659..111944364,3	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10166773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10169613	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10189015	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs10199020	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10211562	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10439381	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10439396	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1054873	0.81[JPT][hapmap]
rs11123407	0.82[ASN][1000 genomes]
rs11674517	0.81[JPT][hapmap]
rs11899831	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398360	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1439287	0.81[JPT][hapmap]
rs1821968	0.81[JPT][hapmap]
rs1837366	0.81[JPT][hapmap]
rs1837367	0.81[JPT][hapmap]
rs1837369	0.81[JPT][hapmap]
rs2165107	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241842	0.81[JPT][hapmap]
rs28723045	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789061	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3789064	0.83[ASN][1000 genomes]
rs3789065	0.82[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3789068	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs3898882	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4627572	0.81[JPT][hapmap]
rs4848406	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849402	0.81[JPT][hapmap]
rs55878194	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs586283	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60982612	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650588	0.83[TSI][hapmap]
rs6542350	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708784	0.86[ASN][1000 genomes]
rs6726007	0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6732491	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6734942	0.83[ASN][1000 genomes]
rs6754738	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6755484	0.85[CEU][hapmap];0.94[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6760053	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs744530	0.86[MEX][hapmap]
rs7562480	0.87[EUR][1000 genomes]
rs7565445	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7565457	0.88[EUR][1000 genomes]
rs7565473	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567184	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7569300	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7572367	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581735	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7585054	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7588534	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7596789	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs879623	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs938095	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9808225	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs9308742	SULT1C2	cis	cerebellum	SCAN
rs9308742	BCL2L11	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111933600-111945200	Enhancers	Fetal Intestine Small	intestine
2	chr2:111934000-111945000	Enhancers	Fetal Intestine Large	intestine
3	chr2:111939400-111944400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr2:111939400-111945400	Enhancers	Pancreas	Pancrea
5	chr2:111941600-111944400	Enhancers	Esophagus	oesophagus
6	chr2:111942000-111946000	Enhancers	Adipose Nuclei	Adipose
7	chr2:111942200-111943800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:111942400-111943800	Enhancers	Liver	Liver
9	chr2:111942400-111943800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr2:111942400-111944000	Enhancers	Placenta	Placenta
11	chr2:111942400-111944200	Weak transcription	Lung	lung
12	chr2:111942400-111945200	Enhancers	Left Ventricle	heart
13	chr2:111942800-111944200	Enhancers	A549	lung
14	chr2:111942800-111944600	Enhancers	Stomach Mucosa	stomach
15	chr2:111943000-111944000	Enhancers	K562	blood
16	chr2:111943000-111944200	Enhancers	Spleen	Spleen
17	chr2:111943000-111944400	Enhancers	Gastric	stomach
18	chr2:111943000-111944800	Enhancers	Fetal Heart	heart
19	chr2:111943000-111945000	Enhancers	Right Ventricle	heart
20	chr2:111943200-111944600	Enhancers	Right Atrium	heart
21	chr2:111943200-111947200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:111943400-111943800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr2:111943400-111944000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:111943400-111944200	Bivalent Enhancer	HepG2	liver
25	chr2:111943400-111945200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:111943600-111943800	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr2:111943600-111943800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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