Variant report

Variant	rs10269174
Chromosome Location	chr7:79034574-79034575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10231862	0.85[EUR][1000 genomes]
rs10240210	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10256590	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10953840	0.85[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs17421752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2190178	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2364916	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427380	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4260838	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730769	0.84[CEU][hapmap]
rs4730806	0.81[MKK][hapmap]
rs6950887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs704865	0.82[EUR][1000 genomes]
rs727390	0.81[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs848904	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs848905	0.82[EUR][1000 genomes]
rs848906	0.82[EUR][1000 genomes]
rs848907	0.82[EUR][1000 genomes]
rs848908	0.82[EUR][1000 genomes]
rs848912	0.84[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs848917	0.84[EUR][1000 genomes]
rs848918	0.83[EUR][1000 genomes]
rs848919	0.88[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs848920	0.89[ASN][1000 genomes]
rs848922	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs848923	0.83[EUR][1000 genomes]
rs848925	0.84[EUR][1000 genomes]
rs848927	0.84[EUR][1000 genomes]
rs848930	0.84[EUR][1000 genomes]
rs848936	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs848937	0.85[CEU][hapmap]
rs848939	0.93[ASN][1000 genomes]
rs848942	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs848943	0.88[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs848952	0.81[EUR][1000 genomes]
rs848954	0.81[EUR][1000 genomes]
rs848955	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs848956	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs860247	0.83[EUR][1000 genomes]
rs991077	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs991260	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9969364	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
5	nsv888514	chr7:78987060-79061837	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv888515	chr7:78987060-79221707	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv607664	chr7:78998409-79057761	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv607665	chr7:79027730-79063644	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv607666	chr7:79029872-79063644	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv607667	chr7:79029872-79065268	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv607668	chr7:79029872-79070452	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10269174	TMEM120A	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79028000-79034600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:79029800-79036400	Enhancers	Liver	Liver
3	chr7:79030800-79034800	Weak transcription	Brain Substantia Nigra	brain
4	chr7:79030800-79036800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr7:79031000-79034800	Weak transcription	Adipose Nuclei	Adipose
6	chr7:79031000-79040800	Weak transcription	Brain Anterior Caudate	brain
7	chr7:79033000-79035000	Enhancers	Brain Hippocampus Middle	brain
8	chr7:79033600-79034600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:79033600-79035200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:79033600-79035600	Weak transcription	Osteobl	bone
11	chr7:79033600-79036200	Weak transcription	Brain Angular Gyrus	brain
12	chr7:79033600-79036400	Weak transcription	Fetal Heart	heart
13	chr7:79033600-79039600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:79033800-79035200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:79033800-79035600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:79033800-79035800	Weak transcription	NHLF	lung
17	chr7:79034200-79036800	Enhancers	HepG2	liver
18	chr7:79034400-79036200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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