Variant report

Variant	rs3735078
Chromosome Location	chr7:150420704-150420705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:150411749..150416479-chr7:150417256..150421069,5	K562	blood:

Variant related genes	Relation type
ENSG00000213203	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11762727	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs11983675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12703097	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13240273	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13240287	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13247782	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17173582	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1860871	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]
rs2041574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075078	0.92[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs2109999	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2159842	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286900	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293172	0.83[GIH][hapmap]
rs2373802	0.84[JPT][hapmap]
rs2373850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34443555	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34531981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35370936	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35662160	0.88[EUR][1000 genomes]
rs3735077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62490382	0.86[EUR][1000 genomes]
rs62490385	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67727004	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6945478	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6971135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6978252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7798682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690530	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9691508	0.83[GIH][hapmap];0.84[JPT][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3735078	CNTNAP2	cis	cerebellum	SCAN
rs3735078	TMEM176B	cis	cerebellum	SCAN
rs3735078	IAN4L1	cis	multi-tissue	Pritchard
rs3735078	TMEM176A	cis	cerebellum	SCAN
rs3735078	GIMAP5	cis	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150414600-150421800	Weak transcription	Fetal Intestine Small	intestine
2	chr7:150415200-150424800	Weak transcription	Pancreas	Pancrea
3	chr7:150415800-150420800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr7:150416200-150420800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
5	chr7:150416800-150422000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:150417400-150423400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:150417800-150422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:150417800-150423400	Weak transcription	Thymus	Thymus
9	chr7:150418000-150424800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr7:150418200-150420800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:150418400-150420800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:150418800-150421400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr7:150419400-150421400	Enhancers	Liver	Liver
14	chr7:150419800-150420800	Enhancers	Adipose Nuclei	Adipose
15	chr7:150419800-150421000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr7:150419800-150421600	Weak transcription	Gastric	stomach
17	chr7:150419800-150423400	Weak transcription	Right Ventricle	heart
18	chr7:150419800-150424400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:150420000-150420800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:150420000-150421400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
21	chr7:150420000-150422000	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr7:150420000-150422000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr7:150420000-150422600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr7:150420000-150423200	Weak transcription	Lung	lung
25	chr7:150420000-150423400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:150420000-150423400	Weak transcription	Fetal Thymus	thymus
27	chr7:150420200-150420800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr7:150420200-150422600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:150420200-150423200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:150420400-150420800	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr7:150420400-150421800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr7:150420400-150422000	Weak transcription	HUVEC	blood vessel
33	chr7:150420600-150421800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr7:150420600-150423400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr7:150420600-150423400	Weak transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links