Variant report

Variant	rs6461387
Chromosome Location	chr7:18898305-18898306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10230371	0.96[MEX][hapmap];0.89[TSI][hapmap]
rs10237149	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10237280	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10237366	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10270210	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10486314	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11761877	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12530943	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12536081	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12536836	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs12699994	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[ASN][1000 genomes]
rs12699998	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12699999	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12700000	0.92[ASN][1000 genomes]
rs12700001	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12700002	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12700003	0.82[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13233322	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13242358	0.90[ASN][1000 genomes]
rs13242758	0.81[AMR][1000 genomes]
rs13245206	0.92[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17349860	0.82[GIH][hapmap];0.80[MEX][hapmap]
rs2028015	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2073964	0.82[JPT][hapmap]
rs2249817	0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes]
rs2286213	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34854568	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3852257	0.84[CHB][hapmap]
rs55761404	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59987684	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60976379	0.83[ASN][1000 genomes]
rs6461386	0.87[CEU][hapmap];0.86[GIH][hapmap];0.81[EUR][1000 genomes]
rs6461389	0.92[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6461390	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6461391	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6461392	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6461393	0.82[AMR][1000 genomes]
rs6461394	0.96[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes]
rs67248060	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6951144	0.88[AMR][1000 genomes]
rs6951522	0.80[GIH][hapmap]
rs6951745	0.84[GIH][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6973029	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs756854	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7794241	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7801037	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs957960	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498112	chr7:18677922-18991946	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv887813	chr7:18720135-18995552	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv523497	chr7:18896011-18959381	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6461387	CTSH	trans	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:18895400-18902800	Weak transcription	Aorta	Aorta
2	chr7:18896200-18900800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:18896600-18901800	Enhancers	NHDF-Ad	bronchial
4	chr7:18896800-18900600	Weak transcription	Osteobl	bone
5	chr7:18897200-18900400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:18897600-18898600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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