Variant report

Variant	rs12700003
Chromosome Location	chr7:18905866-18905867
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10230371	0.81[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs10237149	0.80[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10237280	0.84[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10237366	0.84[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10270210	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10486314	0.95[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12530943	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12536081	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12699994	0.83[MEX][hapmap]
rs12699998	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12699999	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12700001	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12700002	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13233322	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13242758	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13245206	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17349860	0.85[GIH][hapmap]
rs2028015	0.81[GIH][hapmap]
rs2249817	0.85[CEU][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34854568	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59987684	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6461386	0.89[GIH][hapmap];0.83[MKK][hapmap]
rs6461387	0.82[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6461389	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6461390	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6461391	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6461392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6461393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6461394	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67248060	0.82[AMR][1000 genomes]
rs6951144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6951522	0.83[GIH][hapmap]
rs6951745	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6973029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs756854	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7782319	0.87[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs7801037	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7811991	0.91[JPT][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
rs12700003	CTSH	trans	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:18903000-18940000	Weak transcription	Aorta	Aorta
2	chr7:18903800-18907400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:18904600-18906000	Enhancers	Right Atrium	heart
4	chr7:18904800-18907000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:18904800-18907400	Enhancers	Adipose Nuclei	Adipose
6	chr7:18905000-18907000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr7:18905200-18907000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:18905200-18908000	Enhancers	NHDF-Ad	bronchial
9	chr7:18905600-18906600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr7:18905600-18907000	Enhancers	NHLF	lung
11	chr7:18905600-18907200	Enhancers	Osteobl	bone
12	chr7:18905800-18906000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr7:18905800-18906200	Enhancers	Left Ventricle	heart
14	chr7:18905800-18906200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr7:18905800-18907000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:18905800-18907000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:18905800-18907000	Enhancers	Hela-S3	cervix
18	chr7:18905800-18907000	Enhancers	HMEC	breast
19	chr7:18905800-18907000	Enhancers	HSMM	muscle
20	chr7:18905800-18907000	Enhancers	NH-A	brain
21	chr7:18905800-18907200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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