Variant report

Variant	rs12507517
Chromosome Location	chr4:54061989-54061990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11133251	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11133252	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11133257	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs11731676	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs11933772	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12509702	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13152012	0.85[ASN][1000 genomes]
rs1383983	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs1481818	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17705869	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2412397	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412398	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2412400	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2412402	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28795373	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34115081	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4254834	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4472196	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs4515222	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554068	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554072	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554077	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6554089	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs6810608	0.85[ASN][1000 genomes]
rs6818181	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6828377	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6830743	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6834522	0.81[EUR][1000 genomes]
rs6840571	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6846461	0.85[ASN][1000 genomes]
rs71597825	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7654397	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7657388	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs7682970	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7690076	0.82[EUR][1000 genomes]
rs922748	0.91[ASW][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12507517	SPINK2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54043200-54077000	Weak transcription	Primary T cells from cord blood	blood
2	chr4:54048000-54086000	Weak transcription	GM12878-XiMat	blood
3	chr4:54050400-54062400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:54051000-54073000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:54052400-54065800	Weak transcription	Aorta	Aorta
6	chr4:54053000-54093000	Weak transcription	Primary B cells from cord blood	blood
7	chr4:54054600-54072200	Weak transcription	K562	blood
8	chr4:54055800-54062200	Weak transcription	NHLF	lung
9	chr4:54056600-54062400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:54056600-54076400	Weak transcription	Ovary	ovary
11	chr4:54058200-54079800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:54058400-54062200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:54059600-54062400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:54059800-54062400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:54059800-54062400	Weak transcription	Fetal Kidney	kidney
16	chr4:54059800-54062600	Weak transcription	NH-A	brain
17	chr4:54061200-54062400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:54061400-54062600	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:54061600-54062200	Enhancers	NHDF-Ad	bronchial
20	chr4:54061600-54062400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:54061600-54062400	Enhancers	Osteobl	bone
22	chr4:54061600-54063400	Enhancers	Fetal Stomach	stomach
23	chr4:54061800-54062000	Flanking Active TSS	Fetal Lung	lung
24	chr4:54061800-54062200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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