Variant report

Variant	rs11558475
Chromosome Location	chr7:99654600-99654601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11558476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531809	0.82[ASN][1000 genomes]
rs12532238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673441	0.90[MEX][hapmap];0.87[MKK][hapmap];0.82[ASN][1000 genomes]
rs13238380	0.82[ASN][1000 genomes]
rs2261360	0.90[MEX][hapmap];0.81[MKK][hapmap]
rs2897075	0.82[ASN][1000 genomes]
rs35228488	0.82[ASN][1000 genomes]
rs4308665	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4421299	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4727445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729573	0.81[ASN][1000 genomes]
rs4729575	0.82[JPT][hapmap];0.81[MKK][hapmap]
rs55969052	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56054049	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60697181	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67091024	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67110214	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68038211	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963345	0.82[ASN][1000 genomes]
rs72615158	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72615159	0.82[ASN][1000 genomes]
rs73158411	0.81[ASN][1000 genomes]
rs7780686	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796006	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7803317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs941289	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11558475	MCM7	cis	parietal	SCAN
rs11558475	LOC389541	Cis_1M	lymphoblastoid	RTeQTL
rs11558475	OR2AE1	cis	parietal	SCAN
rs11558475	MUC17	cis	parietal	SCAN
rs11558475	AP4M1	cis	cerebellum	SCAN
rs11558475	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs11558475	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs11558475	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs11558475	MBLAC1	cis	cerebellum	SCAN
rs11558475	PILRB	cis	parietal	SCAN

Chromatin state (count:184 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99648000-99654600	Weak transcription	Ovary	ovary
2	chr7:99648200-99654600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:99648200-99654600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:99648200-99654600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr7:99648200-99654600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr7:99648200-99654600	Weak transcription	Aorta	Aorta
7	chr7:99648200-99654600	Weak transcription	Esophagus	oesophagus
8	chr7:99648200-99654600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:99648400-99654600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:99648400-99654600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr7:99648400-99654600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:99648400-99654600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr7:99648400-99654600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr7:99648400-99654600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr7:99648400-99654600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:99648400-99654600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:99648400-99654600	Weak transcription	Adipose Nuclei	Adipose
18	chr7:99648400-99654600	Weak transcription	Colon Smooth Muscle	Colon
19	chr7:99648400-99654600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr7:99648400-99654600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:99648400-99654600	Weak transcription	Gastric	stomach
22	chr7:99648400-99654600	Weak transcription	Left Ventricle	heart
23	chr7:99648400-99654600	Weak transcription	Lung	lung
24	chr7:99648400-99654600	Weak transcription	Pancreas	Pancrea
25	chr7:99648400-99654600	Weak transcription	Right Ventricle	heart
26	chr7:99648400-99654600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:99648400-99654600	Weak transcription	Thymus	Thymus
28	chr7:99648400-99654600	Weak transcription	HUVEC	blood vessel
29	chr7:99648400-99654600	Weak transcription	NH-A	brain
30	chr7:99648400-99654600	Weak transcription	Osteobl	bone
31	chr7:99648400-99654800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:99648400-99654800	Weak transcription	Psoas Muscle	Psoas
33	chr7:99648400-99655000	Weak transcription	Primary B cells from cord blood	blood
34	chr7:99648400-99655000	Weak transcription	Fetal Kidney	kidney
35	chr7:99648400-99655000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr7:99648400-99655000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr7:99648400-99655000	Weak transcription	K562	blood
38	chr7:99648400-99655200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:99648400-99655400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr7:99648400-99655800	Weak transcription	Colonic Mucosa	Colon
41	chr7:99648400-99656200	Weak transcription	Hela-S3	cervix
42	chr7:99648400-99661400	Weak transcription	Small Intestine	intestine
43	chr7:99648400-99667600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr7:99648400-99667600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr7:99648400-99667600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr7:99648400-99667800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr7:99648400-99668000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr7:99648600-99654600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr7:99648600-99654600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:99648600-99654600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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