Variant report

Variant	rs11771962
Chromosome Location	chr7:150316914-150316915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1110093	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11760959	0.81[EUR][1000 genomes]
rs11760960	0.81[EUR][1000 genomes]
rs11761391	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11762727	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11765395	0.81[EUR][1000 genomes]
rs11768988	0.81[EUR][1000 genomes]
rs11769223	0.81[EUR][1000 genomes]
rs11770957	0.81[EUR][1000 genomes]
rs11771561	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11772952	0.81[EUR][1000 genomes]
rs12703077	0.85[CEU][hapmap]
rs12703083	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12703093	0.84[EUR][1000 genomes]
rs12703094	0.84[EUR][1000 genomes]
rs13222905	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13224067	0.81[EUR][1000 genomes]
rs13227870	0.84[EUR][1000 genomes]
rs13231629	0.84[EUR][1000 genomes]
rs13231883	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13232597	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13242186	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs13244793	0.84[EUR][1000 genomes]
rs13247903	0.84[EUR][1000 genomes]
rs1568627	0.91[TSI][hapmap]
rs1860871	0.83[GIH][hapmap]
rs1916022	0.84[EUR][1000 genomes]
rs2041574	0.84[JPT][hapmap]
rs2077672	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2103035	0.84[EUR][1000 genomes]
rs2177188	0.86[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2177189	1.00[ASW][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs2286900	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs2293172	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2293174	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs2373802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2373815	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2373850	0.84[JPT][hapmap]
rs34035420	0.84[EUR][1000 genomes]
rs34211617	0.81[EUR][1000 genomes]
rs34454492	0.84[EUR][1000 genomes]
rs34545650	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34701708	0.82[EUR][1000 genomes]
rs34882694	0.80[EUR][1000 genomes]
rs34921151	0.84[EUR][1000 genomes]
rs35100689	0.84[EUR][1000 genomes]
rs35194540	0.81[EUR][1000 genomes]
rs35225135	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35253919	0.84[EUR][1000 genomes]
rs35302655	0.82[EUR][1000 genomes]
rs35388682	0.81[EUR][1000 genomes]
rs35496043	0.81[EUR][1000 genomes]
rs35556724	0.84[EUR][1000 genomes]
rs35677477	0.81[EUR][1000 genomes]
rs35719526	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35740621	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35790299	0.84[EUR][1000 genomes]
rs36185661	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3735077	0.84[JPT][hapmap]
rs3735078	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs3735079	0.85[CEU][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap]
rs3807378	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4725345	0.81[EUR][1000 genomes]
rs4725348	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4725352	0.84[EUR][1000 genomes]
rs4725353	0.84[EUR][1000 genomes]
rs4725905	0.85[CEU][hapmap];1.00[LWK][hapmap]
rs4725906	0.85[CEU][hapmap]
rs4725921	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4725923	0.81[EUR][1000 genomes]
rs57378599	0.88[AFR][1000 genomes]
rs62491822	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62502270	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73163503	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7800307	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9691508	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[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	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv3388935	chr7:150301204-150374532	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11771962	TMEM176B	cis	cerebellum	SCAN
rs11771962	GIMAP4	cis	lymphoblastoid	seeQTL
rs11771962	MLL3	cis	parietal	SCAN
rs11771962	CNTNAP2	cis	cerebellum	SCAN
rs11771962	ATG9B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150312200-150317000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr7:150312400-150317000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr7:150312400-150321800	Weak transcription	Dnd41	blood
4	chr7:150312600-150317600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:150312600-150317600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:150312800-150317200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr7:150312800-150323000	Weak transcription	Fetal Thymus	thymus
8	chr7:150313400-150317600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr7:150315000-150317000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:150315000-150322200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr7:150316800-150317600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr7:150316800-150317600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr7:150316800-150318000	Enhancers	HUVEC	blood vessel
14	chr7:150316800-150318800	Enhancers	Primary T cells from cord blood	blood
15	chr7:150316800-150318800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:150316800-150320400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:150316800-150320400	Enhancers	Primary T helper cells fromperipheralblood	blood

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