Variant report

Variant	rs12703083
Chromosome Location	chr7:150259959-150259960
allele	C/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	GATA2	chr7:150259735-150260740	HUVEC	blood vessel:	n/a	n/a
2	FOS	chr7:150259824-150260877	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr7:150259671-150260870	HUVEC	blood vessel:	n/a	n/a
4	JUN	chr7:150259849-150260368	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
GIMAP4	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1110093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760959	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11760960	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11761391	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11762727	0.93[CEU][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap]
rs11765395	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11768988	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11769223	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11770957	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11771561	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[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11771962	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11772952	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11982681	0.96[EUR][1000 genomes]
rs12672072	0.96[EUR][1000 genomes]
rs12703077	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs12703078	0.94[EUR][1000 genomes]
rs13222905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13224067	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13231883	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240941	0.96[EUR][1000 genomes]
rs13242186	1.00[CEU][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1568627	0.85[CEU][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap]
rs1568629	0.94[EUR][1000 genomes]
rs1916003	0.96[EUR][1000 genomes]
rs2177188	0.93[CEU][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2177189	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2373802	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2373815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34211617	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34514106	0.96[EUR][1000 genomes]
rs34545650	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35133885	0.96[EUR][1000 genomes]
rs35194540	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35225135	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35388682	0.98[EUR][1000 genomes]
rs35496043	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35556724	0.88[EUR][1000 genomes]
rs35672177	0.96[EUR][1000 genomes]
rs35677477	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36021964	0.96[EUR][1000 genomes]
rs36185661	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3735079	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs3807378	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4725345	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4725348	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4725905	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs4725906	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs4725908	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4725921	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4725923	0.90[EUR][1000 genomes]
rs58414124	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62502270	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62503177	0.96[EUR][1000 genomes]
rs6949485	0.96[EUR][1000 genomes]
rs73163503	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7782113	0.96[EUR][1000 genomes]
rs7802853	0.96[EUR][1000 genomes]
rs7803234	0.96[EUR][1000 genomes]
rs7809438	0.96[EUR][1000 genomes]
rs9691508	0.85[CEU][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1025129	chr7:150146593-150266217	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3395746	chr7:150181141-150300680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv3341786	chr7:150220353-150269134	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv16529	chr7:150249312-150312843	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	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
11	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12703083	ZNF425	cis	cerebellum	SCAN
rs12703083	TMEM176B	cis	cerebellum	SCAN
rs12703083	MLL3	cis	parietal	SCAN
rs12703083	GIMAP4	cis	lymphoblastoid	seeQTL
rs12703083	ATG9B	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150257600-150260400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr7:150258000-150260400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:150258600-150261000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:150258800-150260000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr7:150258800-150260000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr7:150258800-150261600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr7:150259000-150260000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:150259000-150262600	Enhancers	HUVEC	blood vessel
9	chr7:150259200-150260400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr7:150259200-150260400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:150259400-150260800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr7:150259800-150260400	Enhancers	Primary T cells from cord blood	blood
13	chr7:150259800-150261000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:150259800-150261600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr7:150259800-150262600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr7:150259800-150263000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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