Variant report

Variant	rs17438052
Chromosome Location	chr7:40751397-40751398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10251707	1.00[CHB][hapmap]
rs11760481	1.00[ASN][1000 genomes]
rs11760535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761250	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11761336	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11763592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12155334	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17171734	1.00[CHB][hapmap]
rs17437429	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17528214	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17528582	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329818	1.00[CHB][hapmap]
rs34523428	1.00[CHB][hapmap]
rs35456888	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3919491	1.00[CHB][hapmap]
rs4119077	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4119078	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720370	1.00[CHB][hapmap]
rs6462988	1.00[CHB][hapmap]
rs67777497	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6956181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977432	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6977963	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978898	0.85[GIH][hapmap]
rs73124005	0.87[ASN][1000 genomes]
rs73124009	0.87[ASN][1000 genomes]
rs73124018	0.87[ASN][1000 genomes]
rs73124030	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7779570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7800409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7812176	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1025605	chr7:40623026-40789063	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv538823	chr7:40623026-40789063	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1019833	chr7:40649369-40767377	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv538824	chr7:40649369-40767377	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv887988	chr7:40685811-40782572	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17438052	HDGFRP3	trans	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40749000-40754000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr7:40749200-40753200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr7:40749200-40753800	Weak transcription	Osteobl	bone
4	chr7:40749200-40754200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:40749200-40754800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:40749400-40753400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:40749400-40754000	Weak transcription	NHDF-Ad	bronchial
8	chr7:40750600-40751800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:40750800-40752200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:40750800-40752600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:40751000-40752000	Enhancers	HMEC	breast
12	chr7:40751000-40752000	Enhancers	NHEK	skin
13	chr7:40751200-40751400	Weak transcription	Aorta	Aorta
14	chr7:40751200-40751800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr7:40751200-40751800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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