Variant report

Variant	rs1610509
Chromosome Location	chr3:99474327-99474328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10935917	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719468	0.94[JPT][hapmap]
rs1287284	0.87[JPT][hapmap]
rs1384062	0.88[JPT][hapmap]
rs1708167	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1711554	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1711564	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1718235	0.86[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs4577503	0.88[JPT][hapmap]
rs4928230	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs497868	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs498411	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs652026	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs669676	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs704571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704574	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs704577	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629046	0.83[AMR][1000 genomes]
rs792831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792833	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs792835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793439	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs793443	0.88[JPT][hapmap]
rs793446	0.88[JPT][hapmap]
rs793464	0.88[JPT][hapmap]
rs793475	0.84[JPT][hapmap]
rs793481	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793483	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793484	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793485	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793486	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793497	0.88[JPT][hapmap]
rs793502	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs796976	0.88[JPT][hapmap]
rs813218	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][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	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv508231	chr3:99442020-99498951	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1610509	KLKB1	trans	parietal	SCAN
rs1610509	SENP7	cis	parietal	SCAN
rs1610509	ZNF341	trans	cerebellum	SCAN
rs1610509	C3orf26	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99462400-99495600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:99469400-99474600	Genic enhancers	Osteobl	bone
3	chr3:99469400-99478600	Genic enhancers	Muscle Satellite Cultured Cells	--
4	chr3:99471600-99474400	Weak transcription	Aorta	Aorta
5	chr3:99472400-99474400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:99472400-99474400	Weak transcription	NHDF-Ad	bronchial
7	chr3:99472400-99474600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:99472400-99474600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:99472400-99475600	Weak transcription	HMEC	breast
10	chr3:99472400-99476800	Weak transcription	HSMMtube	muscle
11	chr3:99472400-99477000	Weak transcription	Fetal Heart	heart
12	chr3:99472400-99478600	Weak transcription	Right Atrium	heart
13	chr3:99472400-99479000	Weak transcription	Left Ventricle	heart
14	chr3:99472400-99479600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:99472400-99480400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:99472400-99481400	Weak transcription	Psoas Muscle	Psoas
17	chr3:99472400-99484000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:99472400-99484000	Weak transcription	NHLF	lung
19	chr3:99472400-99493000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:99472400-99493000	Weak transcription	NHEK	skin
21	chr3:99472400-99493400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:99472600-99483800	Weak transcription	NH-A	brain
23	chr3:99472800-99479000	Weak transcription	Adipose Nuclei	Adipose
24	chr3:99473000-99477600	Strong transcription	HUVEC	blood vessel
25	chr3:99473400-99475200	Genic enhancers	HSMM	muscle
26	chr3:99473600-99475800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:99474200-99475600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:99474200-99476800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links