Variant report

Variant	rs13230579
Chromosome Location	chr7:78947104-78947105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10225262	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap]
rs10230177	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10234403	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10235211	1.00[CEU][hapmap]
rs10240268	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10241692	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10254948	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10266537	1.00[CEU][hapmap]
rs10270040	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs10270645	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10270764	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs10271328	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10273845	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10480716	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10953797	1.00[CEU][hapmap]
rs10953812	1.00[CEU][hapmap]
rs10953821	0.83[ASN][1000 genomes]
rs10953823	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10953825	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10953826	0.85[ASN][1000 genomes]
rs10953827	0.90[ASN][1000 genomes]
rs10953828	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10953835	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11535245	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766918	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768754	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11977493	1.00[CEU][hapmap]
rs12111592	0.87[ASN][1000 genomes]
rs12111980	0.87[ASN][1000 genomes]
rs12154356	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12154470	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12154980	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12216581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12532467	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap]
rs12534590	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12536811	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536914	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12538685	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539220	0.87[CEU][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12540324	0.85[ASN][1000 genomes]
rs12666243	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12706101	0.89[ASN][1000 genomes]
rs12706102	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs13221173	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13222018	0.82[ASN][1000 genomes]
rs13224467	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13224739	0.81[ASN][1000 genomes]
rs13230407	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13234027	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13243285	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13247562	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13306942	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1358473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1406152	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1406157	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1406159	1.00[CEU][hapmap]
rs1528263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1528265	0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1528269	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1528270	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1528271	1.00[CEU][hapmap]
rs1528272	1.00[CEU][hapmap]
rs1528274	1.00[CEU][hapmap]
rs1554833	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1554834	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1554835	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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554836	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881292	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1881296	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1918937	1.00[CEU][hapmap]
rs1918939	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs2058393	1.00[CEU][hapmap]
rs2159709	1.00[CEU][hapmap]
rs2190179	0.82[JPT][hapmap]
rs2242505	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2364902	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs28410701	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2886212	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34059048	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34066812	0.85[ASN][1000 genomes]
rs34983504	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35035926	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35512002	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4129689	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4143262	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4256536	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4445162	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4727838	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4727841	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4727843	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730746	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs4730747	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs4730806	0.82[JPT][hapmap]
rs58309104	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62458964	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62458973	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6466593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466597	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6946286	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.83[ASN][1000 genomes]
rs6946789	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952164	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap]
rs6953483	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs6953771	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs6961357	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6965742	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71531164	0.85[ASN][1000 genomes]
rs717067	1.00[CEU][hapmap]
rs7341488	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7459140	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7779953	1.00[CEU][hapmap]
rs7782460	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7782585	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs7790555	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7809944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs949496	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9648980	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9886146	0.89[ASN][1000 genomes]
rs9886330	0.89[ASN][1000 genomes]
rs991259	0.82[JPT][hapmap]
rs993860	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1029799	chr7:78608097-79061737	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv831041	chr7:78819499-78973222	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2764028	chr7:78874740-79112630	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv971531	chr7:78944995-78949430	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13230579	TMEM120A	cis	cerebellum	SCAN
rs13230579	MAGI2	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78946400-78947600	Enhancers	Liver	Liver
2	chr7:78946600-78947600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr7:78946600-78947600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr7:78946600-78949400	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr7:78946800-78947400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr7:78946800-78947400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:78946800-78947400	Enhancers	Brain Hippocampus Middle	brain
8	chr7:78946800-78947600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr7:78946800-78947600	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr7:78946800-78947600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr7:78946800-78947600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:78946800-78947600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:78946800-78947600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:78946800-78947600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:78946800-78947600	Flanking Active TSS	A549	lung
16	chr7:78946800-78947600	Enhancers	HMEC	breast
17	chr7:78946800-78947600	Enhancers	HUVEC	blood vessel
18	chr7:78946800-78947600	Enhancers	Osteobl	bone
19	chr7:78946800-78948000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:78946800-78948000	Enhancers	HepG2	liver
21	chr7:78947000-78947400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr7:78947000-78947400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:78947000-78947400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:78947000-78947400	Enhancers	H9 Cell Line	embryonic stem cell
25	chr7:78947000-78947400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:78947000-78947400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr7:78947000-78947400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr7:78947000-78947400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:78947000-78947400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:78947000-78947400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:78947000-78947400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:78947000-78947400	Enhancers	Aorta	Aorta
33	chr7:78947000-78947400	Enhancers	Brain Angular Gyrus	brain
34	chr7:78947000-78947400	Enhancers	Brain Substantia Nigra	brain
35	chr7:78947000-78947400	Enhancers	Ovary	ovary
36	chr7:78947000-78947400	Enhancers	Stomach Smooth Muscle	stomach
37	chr7:78947000-78947400	Enhancers	HSMMtube	muscle
38	chr7:78947000-78947600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:78947000-78947600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr7:78947000-78947600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr7:78947000-78947600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:78947000-78947600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr7:78947000-78947600	Enhancers	NHEK	skin
44	chr7:78947000-78947600	Enhancers	NHLF	lung
45	chr7:78947000-78947800	Enhancers	NH-A	brain
46	chr7:78947000-78947800	Enhancers	NHDF-Ad	bronchial
47	chr7:78947000-78948000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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