Variant report

Variant	rs10992161
Chromosome Location	chr9:94687927-94687928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10820916	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820917	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10820919	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10820921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820922	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10820928	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10820933	0.84[CEU][hapmap]
rs10820934	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs10820939	0.85[CEU][hapmap]
rs10992158	0.96[TSI][hapmap]
rs10992162	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10992165	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10992166	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992218	0.85[CEU][hapmap]
rs10992219	0.85[CEU][hapmap]
rs10992224	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap]
rs11789973	0.82[TSI][hapmap]
rs11790991	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap]
rs12554679	0.95[CEU][hapmap];0.81[JPT][hapmap]
rs12683797	0.86[TSI][hapmap]
rs1534534	0.86[CEU][hapmap]
rs1892263	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919101	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3932420	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4430151	0.86[TSI][hapmap]
rs56013831	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56272949	0.91[EUR][1000 genomes]
rs56280154	0.92[EUR][1000 genomes]
rs56309039	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62565755	0.93[EUR][1000 genomes]
rs62567925	0.81[EUR][1000 genomes]
rs7034006	0.86[CEU][hapmap];1.00[GIH][hapmap]
rs7038397	0.82[CEU][hapmap];1.00[GIH][hapmap]
rs7038823	0.86[CEU][hapmap]
rs72746299	0.94[EUR][1000 genomes]
rs7857759	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap]
rs7862013	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7866775	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7871522	0.86[CEU][hapmap];1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv530946	chr9:94633154-94715023	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10992161	SPTLC1	cis	parietal	SCAN
rs10992161	NXNL2	cis	parietal	SCAN
rs10992161	BARX1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94681400-94691400	Weak transcription	Pancreas	Pancrea
2	chr9:94683600-94691800	Weak transcription	Fetal Lung	lung
3	chr9:94683600-94692000	Weak transcription	K562	blood
4	chr9:94685400-94690400	Weak transcription	Fetal Intestine Small	intestine
5	chr9:94686400-94689200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:94686400-94692400	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:94686600-94690400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:94686600-94690600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:94686600-94690800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:94686600-94696000	Weak transcription	Ovary	ovary
11	chr9:94686800-94688400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:94686800-94690200	Weak transcription	Fetal Stomach	stomach
13	chr9:94687400-94688200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:94687600-94688000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:94687600-94688000	Enhancers	Gastric	stomach
16	chr9:94687600-94688200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:94687800-94689000	Weak transcription	Stomach Smooth Muscle	stomach

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