Variant report

Variant	rs9691508
Chromosome Location	chr7:150330269-150330270
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11761391	0.94[AFR][1000 genomes]
rs11762727	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11771561	0.85[CEU][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap]
rs11771962	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12703077	0.92[CEU][hapmap]
rs12703083	0.85[CEU][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap]
rs12703093	0.99[EUR][1000 genomes]
rs12703094	0.99[EUR][1000 genomes]
rs13222905	0.85[CEU][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap]
rs13227870	0.99[EUR][1000 genomes]
rs13231629	0.99[EUR][1000 genomes]
rs13231883	0.85[CEU][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap]
rs13232597	0.85[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs13242186	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[GIH][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs13244793	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13247903	0.99[EUR][1000 genomes]
rs1860871	0.83[GIH][hapmap]
rs1916022	0.99[EUR][1000 genomes]
rs2041574	0.84[JPT][hapmap]
rs2077672	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2103035	0.99[EUR][1000 genomes]
rs2177189	1.00[ASW][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs2286900	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs2293172	0.85[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap]
rs2293174	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs2373802	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2373815	0.85[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs2373850	0.84[JPT][hapmap]
rs34035420	0.99[EUR][1000 genomes]
rs34454492	0.99[EUR][1000 genomes]
rs34545650	0.81[AFR][1000 genomes]
rs34701708	0.97[EUR][1000 genomes]
rs34882694	0.95[EUR][1000 genomes]
rs34921151	0.99[EUR][1000 genomes]
rs35100689	0.99[EUR][1000 genomes]
rs35225135	0.85[AMR][1000 genomes]
rs35253919	0.99[EUR][1000 genomes]
rs35302655	0.97[EUR][1000 genomes]
rs35719526	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35740621	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35790299	0.99[EUR][1000 genomes]
rs3735077	0.84[JPT][hapmap]
rs3735078	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs3735079	0.92[CEU][hapmap]
rs4725348	0.94[AFR][1000 genomes]
rs4725352	0.99[EUR][1000 genomes]
rs4725353	0.99[EUR][1000 genomes]
rs4725905	0.92[CEU][hapmap]
rs4725906	0.92[CEU][hapmap]
rs57378599	0.88[AFR][1000 genomes]
rs62491822	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7800307	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9691508	GIMAP5	cis	lymphoblastoid	seeQTL
rs9691508	MLL3	cis	parietal	SCAN
rs9691508	TMEM176B	cis	cerebellum	SCAN
rs9691508	GIMAP4	cis	lymphoblastoid	seeQTL
rs9691508	CNTNAP2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150329400-150330400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr7:150329600-150330400	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr7:150329600-150330400	Flanking Active TSS	Dnd41	blood
4	chr7:150329600-150330600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr7:150329600-150330600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr7:150329600-150330600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr7:150329800-150330600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr7:150329800-150340200	Weak transcription	Left Ventricle	heart
9	chr7:150330000-150330400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr7:150330000-150330400	Enhancers	HUVEC	blood vessel
11	chr7:150330000-150330600	Enhancers	Primary hematopoietic stem cells	blood
12	chr7:150330000-150330600	Enhancers	Fetal Thymus	thymus
13	chr7:150330000-150330800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr7:150330000-150331200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:150330000-150331400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:150330000-150332000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr7:150330000-150332200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:150330200-150331000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr7:150330200-150331000	Enhancers	GM12878-XiMat	blood
20	chr7:150330200-150331200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:150330200-150332000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:150330200-150332200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:150330200-150332200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr7:150330200-150332400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:150330200-150332400	Enhancers	Primary T killer memory cells from peripheral blood	blood

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