Variant report

Variant	rs2242505
Chromosome Location	chr7:78918634-78918635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10225262	1.00[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs10230177	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10232677	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10234403	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10235211	1.00[CEU][hapmap]
rs10240268	0.87[ASN][1000 genomes]
rs10241692	0.85[ASN][1000 genomes]
rs10266537	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs10270040	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap]
rs10270645	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10270764	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10271328	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10273845	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs10480716	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10499842	0.91[YRI][hapmap]
rs10953797	1.00[CEU][hapmap]
rs10953812	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs10953821	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10953823	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10953825	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10953826	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10953827	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10953828	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10953835	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs11532779	0.84[EUR][1000 genomes]
rs11535245	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11763567	0.91[YRI][hapmap]
rs11766918	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11768754	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11977493	1.00[CEU][hapmap]
rs12111592	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12111980	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12154356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12154470	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12154980	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12216581	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12532467	1.00[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap]
rs12534590	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12536811	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12536914	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12538685	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12539220	0.87[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12540324	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12666243	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12706101	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12706102	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13221173	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13222018	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13224467	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13224739	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13230407	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13230579	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]
rs13234027	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13240307	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13243285	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13247562	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13306942	0.82[ASN][1000 genomes]
rs1358473	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1406152	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1406157	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1406159	1.00[CEU][hapmap]
rs1528263	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1528265	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1528269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1528270	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1528271	1.00[CEU][hapmap]
rs1528272	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs1528274	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs1528281	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1554833	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1554834	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1554835	0.80[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554836	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1881292	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs1881296	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1918937	1.00[CEU][hapmap]
rs1918938	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1918939	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2058393	1.00[CEU][hapmap]
rs2069132	0.91[YRI][hapmap]
rs2107992	0.81[YRI][hapmap]
rs2158707	0.81[YRI][hapmap]
rs2159709	1.00[CEU][hapmap]
rs2190179	0.82[JPT][hapmap]
rs2364902	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28410701	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2886212	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs34059048	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34066812	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34263368	0.83[EUR][1000 genomes]
rs34983504	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35035926	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35512002	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3884514	0.86[YRI][hapmap]
rs4129689	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4143262	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs4256536	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4445162	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4727838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4727841	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4727843	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730746	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4730747	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4730806	0.82[JPT][hapmap]
rs58309104	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62458964	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6946286	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6946789	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6952164	1.00[CEU][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs6953105	0.81[YRI][hapmap]
rs6953483	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs6953771	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs6968269	0.89[EUR][1000 genomes]
rs71531164	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs717067	1.00[CEU][hapmap]
rs7341488	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7455235	0.89[EUR][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];0.93[TSI][hapmap]
rs7790555	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7797165	0.81[YRI][hapmap]
rs7809944	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9640776	0.86[YRI][hapmap]
rs9641579	0.91[YRI][hapmap]
rs9641583	0.81[YRI][hapmap]
rs9641589	0.81[YRI][hapmap]
rs9648980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9886146	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9886330	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs991259	0.82[JPT][hapmap]
rs993860	0.82[JPT][hapmap]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2242505	TMEM120A	cis	cerebellum	SCAN
rs2242505	MAGI2	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78912000-78922200	Weak transcription	Brain Angular Gyrus	brain
2	chr7:78913400-78920600	Weak transcription	HUVEC	blood vessel
3	chr7:78913800-78919800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:78913800-78920000	Weak transcription	NH-A	brain
5	chr7:78913800-78922400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:78913800-78923000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:78915400-78919800	Weak transcription	A549	lung
8	chr7:78915400-78920200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:78915400-78920600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:78915600-78919800	Weak transcription	HMEC	breast
11	chr7:78915800-78919800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:78915800-78919800	Weak transcription	NHEK	skin
13	chr7:78915800-78920600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:78917400-78918800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:78918200-78919800	Weak transcription	Osteobl	bone
16	chr7:78918200-78922200	Weak transcription	Adipose Nuclei	Adipose
17	chr7:78918400-78920600	Weak transcription	NHLF	lung
18	chr7:78918400-78922200	Weak transcription	Brain Substantia Nigra	brain
19	chr7:78918600-78919800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:78918600-78920000	Weak transcription	NHDF-Ad	bronchial
21	chr7:78918600-78920400	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:78918600-78920800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:78918600-78922200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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