Variant report

Variant	rs848936
Chromosome Location	chr7:78983840-78983841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10231862	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10256590	0.83[EUR][1000 genomes]
rs10269174	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs10485956	0.82[YRI][hapmap]
rs10953840	1.00[CEU][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11976160	0.82[YRI][hapmap]
rs11980940	0.82[YRI][hapmap]
rs13228109	0.90[YRI][hapmap]
rs13231892	0.82[YRI][hapmap]
rs1406151	0.86[JPT][hapmap]
rs17152303	0.91[JPT][hapmap]
rs17152310	0.86[JPT][hapmap]
rs17152326	0.86[JPT][hapmap]
rs17152429	0.82[YRI][hapmap]
rs17152446	0.82[YRI][hapmap]
rs17421752	0.81[EUR][1000 genomes]
rs2364916	0.81[EUR][1000 genomes]
rs28427380	0.81[EUR][1000 genomes]
rs4260838	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4730769	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4730807	0.82[YRI][hapmap]
rs6950887	0.85[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs704865	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804381	0.86[JPT][hapmap]
rs7804560	0.91[JPT][hapmap]
rs848904	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848905	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848906	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848907	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs848908	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848912	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs848917	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848918	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848919	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs848920	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs848922	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848923	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848925	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848927	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848930	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848937	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs848939	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs848942	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs848943	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs848949	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848952	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848954	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848955	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs848956	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860247	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9692383	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs991077	0.91[EUR][1000 genomes]
rs991260	0.89[EUR][1000 genomes]
rs9969364	0.85[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv464600	chr7:78981719-79030922	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv607663	chr7:78981719-79030922	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv888513	chr7:78983840-79023504	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs848936	TMEM120A	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78980800-78986200	Weak transcription	Brain Substantia Nigra	brain
2	chr7:78982000-78986000	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:78982000-78992000	Weak transcription	NHLF	lung
4	chr7:78982200-78986000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:78982200-78986200	Weak transcription	Brain Anterior Caudate	brain
6	chr7:78982400-78986400	Weak transcription	Fetal Heart	heart
7	chr7:78982600-78986000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr7:78983000-78985400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:78983000-78986600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:78983400-78986200	Weak transcription	Brain Angular Gyrus	brain

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