Variant report

Variant	rs7800409
Chromosome Location	chr7:40738576-40738577
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10251707	1.00[CHB][hapmap]
rs11760535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11761250	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11761336	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11763592	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11768774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[MEX][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11772576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12155334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17171734	1.00[CHB][hapmap]
rs17437429	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17438052	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]
rs17528214	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17528582	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2329818	1.00[CHB][hapmap]
rs34523428	1.00[CHB][hapmap]
rs35456888	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3919491	1.00[CHB][hapmap]
rs4119077	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4119078	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4720370	1.00[CHB][hapmap]
rs6462988	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs67777497	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6956181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6977432	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6977963	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6978898	0.82[GIH][hapmap]
rs73124030	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7779570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812176	0.93[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv887987	chr7:40505382-40748650	Enhancers Weak transcription Active TSS Flanking 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
3	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
4	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
5	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
6	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
7	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
rs7800409	HDGFRP3	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40734600-40740800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr7:40737200-40738600	Enhancers	NHEK	skin
3	chr7:40737200-40739000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:40737200-40739200	Enhancers	HMEC	breast
5	chr7:40737200-40742200	Enhancers	Osteobl	bone
6	chr7:40737200-40742400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr7:40737400-40738600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:40737400-40738600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:40737600-40738600	Enhancers	NHDF-Ad	bronchial
10	chr7:40737800-40738600	Enhancers	HSMMtube	muscle
11	chr7:40738000-40738600	Enhancers	NH-A	brain
12	chr7:40738000-40739000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr7:40738200-40738600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr7:40738200-40739800	Weak transcription	HSMM	muscle
15	chr7:40738200-40740400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:40738200-40740400	Weak transcription	Aorta	Aorta
17	chr7:40738200-40740600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:40738400-40738800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:40738400-40740200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:40738400-40740400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:40738400-40746000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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