Variant report

Variant	rs7688646
Chromosome Location	chr4:54100965-54100966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10517291	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs10517292	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs11133246	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11133247	0.88[ASN][1000 genomes]
rs11929903	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11947928	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12108246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12499016	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12499731	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12500564	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12503963	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12505661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507228	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512359	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12512748	0.85[AMR][1000 genomes]
rs12640471	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12646150	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12647441	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12650397	0.86[ASN][1000 genomes]
rs17082453	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.89[MEX][hapmap]
rs17082476	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17082504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17082529	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17082549	0.85[AMR][1000 genomes]
rs17082565	0.93[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs1987028	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2001881	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs2128103	0.83[CHD][hapmap]
rs34019927	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4299650	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4419530	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4421047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4515221	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4529117	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4864451	0.93[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4864452	0.85[AMR][1000 genomes]
rs4864453	0.93[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs4864454	0.85[AMR][1000 genomes]
rs4864747	1.00[ASW][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs6826467	0.93[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.85[AMR][1000 genomes]
rs6830879	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6854446	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73143456	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73143458	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73143484	0.88[ASN][1000 genomes]
rs73147378	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73147396	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73149212	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs751265	0.93[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs7664488	0.81[ASN][1000 genomes]
rs7687029	0.85[AMR][1000 genomes]
rs7696426	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.89[MEX][hapmap]
rs9761301	0.87[AMR][1000 genomes]
rs9762074	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv997614	chr4:54086727-54150632	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv879013	chr4:54093717-54137228	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7688646	SPINK2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54064400-54106600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:54077800-54107600	Weak transcription	Lung	lung
3	chr4:54078000-54107200	Weak transcription	Primary T cells from cord blood	blood
4	chr4:54090000-54107200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:54093800-54110800	Weak transcription	Primary B cells from cord blood	blood
6	chr4:54094400-54106600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:54094600-54103400	Weak transcription	K562	blood
8	chr4:54096800-54104800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:54097200-54101000	Weak transcription	Left Ventricle	heart
10	chr4:54099000-54101200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:54099200-54107200	Weak transcription	Psoas Muscle	Psoas
12	chr4:54099600-54106600	Weak transcription	NHDF-Ad	bronchial
13	chr4:54099800-54101200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:54099800-54102400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr4:54099800-54107200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:54100000-54106600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:54100200-54101600	Enhancers	NHEK	skin
18	chr4:54100200-54111600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:54100600-54101800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:54100800-54101200	Enhancers	GM12878-XiMat	blood
21	chr4:54100800-54101400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:54100800-54101600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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