Variant report

Variant	rs1860871
Chromosome Location	chr7:150389593-150389594
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150380547..150382670-chr7:150386657..150389613,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10232092	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11762727	0.83[GIH][hapmap]
rs11983675	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12703095	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12703097	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13240273	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13240287	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13247782	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17173582	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2041574	0.88[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2075078	0.83[JPT][hapmap]
rs2109999	0.83[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2159842	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2286900	0.88[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2293172	0.83[GIH][hapmap]
rs2373850	0.88[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34443555	0.86[AMR][1000 genomes]
rs34531981	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35370936	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35662160	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3735077	0.88[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3735078	0.88[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55821597	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62490382	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62490385	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67727004	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6945478	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6953961	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6971135	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6978252	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7798682	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9690530	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9691508	0.83[GIH][hapmap]

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	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
8	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
9	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1860871	CNTNAP2	cis	cerebellum	SCAN
rs1860871	TMEM176B	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150383600-150389600	Weak transcription	Fetal Muscle Leg	muscle
2	chr7:150383600-150390800	Weak transcription	Small Intestine	intestine
3	chr7:150383600-150391000	Weak transcription	Gastric	stomach
4	chr7:150383600-150391400	Weak transcription	Brain Substantia Nigra	brain
5	chr7:150383800-150392200	Weak transcription	Right Atrium	heart
6	chr7:150383800-150392200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr7:150384200-150390600	ZNF genes & repeats	GM12878-XiMat	blood
8	chr7:150385000-150391600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:150385200-150390400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr7:150385200-150390400	Weak transcription	HUVEC	blood vessel
11	chr7:150385600-150390000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:150385600-150390000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:150385800-150390600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:150385800-150391200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr7:150385800-150392200	Weak transcription	Brain Hippocampus Middle	brain
16	chr7:150386000-150390200	Strong transcription	Liver	Liver
17	chr7:150386200-150391200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:150386600-150389800	Strong transcription	Thymus	Thymus
19	chr7:150386600-150391200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
20	chr7:150387000-150393200	ZNF genes & repeats	Primary T cells from cord blood	blood
21	chr7:150387200-150389800	Strong transcription	Adipose Nuclei	Adipose
22	chr7:150387200-150390000	ZNF genes & repeats	Lung	lung
23	chr7:150387200-150390200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr7:150387200-150390200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
25	chr7:150387200-150391200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
26	chr7:150387200-150393600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
27	chr7:150387600-150390600	Genic enhancers	Dnd41	blood
28	chr7:150387600-150391400	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr7:150387800-150390200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:150387800-150390400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
31	chr7:150387800-150391200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
32	chr7:150388000-150390200	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
33	chr7:150388000-150391200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
34	chr7:150388000-150391200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
35	chr7:150388200-150390000	ZNF genes & repeats	Fetal Thymus	thymus
36	chr7:150388200-150390200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:150388200-150390400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
38	chr7:150388200-150390600	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:150388200-150391200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
40	chr7:150388200-150391600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr7:150388400-150389800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr7:150388400-150390000	Weak transcription	Colon Smooth Muscle	Colon
43	chr7:150388400-150390200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
44	chr7:150388400-150392200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:150388600-150389600	Weak transcription	Colonic Mucosa	Colon
46	chr7:150388600-150389600	Weak transcription	Placenta	Placenta
47	chr7:150388600-150390000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:150389000-150389600	Weak transcription	Fetal Lung	lung
49	chr7:150389200-150390000	ZNF genes & repeats	Spleen	Spleen
50	chr7:150389400-150389600	ZNF genes & repeats	Fetal Stomach	stomach

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