Variant report

Variant	rs11762727
Chromosome Location	chr7:150324157-150324158
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11761391	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11771561	0.93[CEU][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap]
rs11771962	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12703077	0.85[CEU][hapmap]
rs12703083	0.93[CEU][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap]
rs12703093	0.92[EUR][1000 genomes]
rs12703094	0.92[EUR][1000 genomes]
rs13222905	0.93[CEU][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap]
rs13227870	0.92[EUR][1000 genomes]
rs13231629	0.92[EUR][1000 genomes]
rs13231883	0.93[CEU][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap]
rs13232597	0.93[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs13242186	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs13244793	0.92[EUR][1000 genomes]
rs13247903	0.92[EUR][1000 genomes]
rs1860871	0.83[GIH][hapmap]
rs1916022	0.92[EUR][1000 genomes]
rs2041574	0.84[JPT][hapmap]
rs2077672	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2103035	0.92[EUR][1000 genomes]
rs2177188	0.86[CEU][hapmap]
rs2177189	1.00[ASW][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs2286900	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs2293172	0.93[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs2293174	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs2373802	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2373815	0.93[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs2373850	0.84[JPT][hapmap]
rs34035420	0.92[EUR][1000 genomes]
rs34454492	0.92[EUR][1000 genomes]
rs34545650	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs34701708	0.90[EUR][1000 genomes]
rs34882694	0.89[EUR][1000 genomes]
rs34921151	0.92[EUR][1000 genomes]
rs35100689	0.92[EUR][1000 genomes]
rs35225135	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35253919	0.92[EUR][1000 genomes]
rs35302655	0.90[EUR][1000 genomes]
rs35719526	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35740621	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35790299	0.92[EUR][1000 genomes]
rs36185661	0.82[AMR][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]
rs4725348	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4725352	0.92[EUR][1000 genomes]
rs4725353	0.92[EUR][1000 genomes]
rs4725905	0.85[CEU][hapmap];1.00[LWK][hapmap]
rs4725906	0.85[CEU][hapmap]
rs4725921	0.81[AMR][1000 genomes]
rs57378599	0.88[AFR][1000 genomes]
rs62491822	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7800307	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9691508	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]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11762727	CNTNAP2	cis	cerebellum	SCAN
rs11762727	ATG9B	cis	parietal	SCAN
rs11762727	GIMAP4	cis	lymphoblastoid	seeQTL
rs11762727	MLL3	cis	parietal	SCAN
rs11762727	TMEM176B	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150320400-150324400	Weak transcription	Gastric	stomach
2	chr7:150320600-150324400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr7:150321800-150324600	Weak transcription	Fetal Stomach	stomach
4	chr7:150321800-150326800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr7:150322200-150328400	Weak transcription	Fetal Intestine Small	intestine
6	chr7:150322600-150326800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr7:150323000-150325600	Strong transcription	Fetal Thymus	thymus
8	chr7:150323000-150326000	Strong transcription	HUVEC	blood vessel
9	chr7:150323200-150324400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:150323200-150324400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr7:150323200-150324600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr7:150323200-150326200	Genic enhancers	Lung	lung
13	chr7:150323200-150327200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:150323200-150327400	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr7:150323200-150327400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
16	chr7:150323200-150327600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:150323200-150327600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr7:150323200-150327800	Genic enhancers	Spleen	Spleen
19	chr7:150323400-150324200	Genic enhancers	Monocytes-CD14+_RO01746	blood
20	chr7:150323400-150326200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr7:150323400-150327600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:150323400-150327600	Genic enhancers	Primary monocytes fromperipheralblood	blood
23	chr7:150323400-150327600	Strong transcription	Thymus	Thymus
24	chr7:150323400-150327800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr7:150323400-150328200	Weak transcription	Brain Substantia Nigra	brain
26	chr7:150323600-150324400	Genic enhancers	Primary hematopoietic stem cells	blood
27	chr7:150323600-150324600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr7:150323600-150325400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:150323600-150327200	Genic enhancers	Adipose Nuclei	Adipose
30	chr7:150323600-150327400	Enhancers	Right Atrium	heart
31	chr7:150323600-150328000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
32	chr7:150323800-150324200	Enhancers	Right Ventricle	heart
33	chr7:150323800-150324200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr7:150323800-150324800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
35	chr7:150323800-150324800	Strong transcription	Placenta	Placenta
36	chr7:150323800-150325000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:150323800-150326400	Genic enhancers	Left Ventricle	heart
38	chr7:150323800-150328000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr7:150323800-150328400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr7:150324000-150324400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr7:150324000-150325200	Strong transcription	Fetal Muscle Leg	muscle
42	chr7:150324000-150326400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr7:150324000-150326400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
44	chr7:150324000-150327600	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
45	chr7:150324000-150327600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr7:150324000-150329200	Transcr. at gene 5' and 3'	Dnd41	blood

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