Variant report

Variant	rs957960
Chromosome Location	chr7:18877408-18877409
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10237149	0.82[GIH][hapmap]
rs12536836	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540774	0.87[EUR][1000 genomes]
rs13238389	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13245206	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs17349860	0.91[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2016515	0.87[GIH][hapmap]
rs2073963	0.94[ASW][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2073965	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3852256	0.87[CHB][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3852257	0.82[EUR][1000 genomes]
rs6461386	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[ASN][1000 genomes]
rs6461387	0.87[CEU][hapmap]
rs6461389	0.86[JPT][hapmap]
rs6951522	0.95[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs756853	0.84[LWK][hapmap]
rs756854	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs7795433	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7811991	0.86[JPT][hapmap]
rs957958	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv887814	chr7:18751998-18886177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs957960	CTSH	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:18866800-18885200	Weak transcription	Primary B cells from cord blood	blood
2	chr7:18867200-18882400	Weak transcription	Left Ventricle	heart
3	chr7:18868200-18879400	Weak transcription	HSMMtube	muscle
4	chr7:18868800-18887400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:18875600-18888000	Weak transcription	Aorta	Aorta

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