Variant report

Variant	rs6493158
Chromosome Location	chr15:45841616-45841617
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45841609..45843950-chr15:45877578..45879390,2	K562	blood:
2	chr15:45839175..45843127-chr15:45877708..45881310,7	K562	blood:
3	chr15:45790676..45792574-chr15:45839895..45841978,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260170	Chromatin interaction
ENSG00000104164	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10152697	0.86[CHB][hapmap]
rs10851425	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1153829	0.93[JPT][hapmap]
rs1153830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1153831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1153832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1288861	0.88[CHB][hapmap]
rs1288863	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1288865	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13376	0.83[LWK][hapmap]
rs1442797	0.81[LWK][hapmap]
rs1529354	0.80[YRI][hapmap]
rs16944305	0.80[YRI][hapmap]
rs16944629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16945605	0.84[YRI][hapmap]
rs16952731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs17535381	0.88[CHB][hapmap]
rs17537244	0.93[CEU][hapmap];0.88[CHB][hapmap]
rs1768458	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2088164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2433600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2433617	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2433619	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2486287	0.88[CHB][hapmap]
rs35828336	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4448883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55997350	0.89[EUR][1000 genomes]
rs56179992	0.97[EUR][1000 genomes]
rs56405528	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59574269	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60350201	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60992352	0.97[EUR][1000 genomes]
rs61193305	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493154	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493157	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];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493160	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7165838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7169748	1.00[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7170090	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7171406	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7173983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7183382	0.81[LWK][hapmap]
rs719019	0.81[LWK][hapmap]
rs72711278	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72711279	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72711280	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72711283	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72711284	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711290	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72711294	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72711301	0.97[EUR][1000 genomes]
rs72713103	0.97[EUR][1000 genomes]
rs72713104	0.96[EUR][1000 genomes]
rs72713105	0.96[EUR][1000 genomes]
rs7342662	0.81[LWK][hapmap]
rs8023437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8025407	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs8025600	0.81[LWK][hapmap]
rs8029509	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8040466	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8042662	0.83[YRI][hapmap]
rs8042811	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9972498	0.88[CHB][hapmap]

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	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1045556	chr15:45777396-45884854	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6493158	TMEM62	cis	cerebellum	SCAN
rs6493158	RPAP1	cis	cerebellum	SCAN
rs6493158	MGA	cis	parietal	SCAN
rs6493158	GPR176	cis	cerebellum	SCAN
rs6493158	FAM82A2	cis	cerebellum	SCAN
rs6493158	SLC30A4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45838400-45841800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:45840600-45842800	Enhancers	HSMMtube	muscle
3	chr15:45841000-45842400	Enhancers	NHDF-Ad	bronchial
4	chr15:45841200-45841800	Enhancers	Hela-S3	cervix
5	chr15:45841200-45841800	Enhancers	HSMM	muscle
6	chr15:45841200-45844600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:45841400-45842200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:45841400-45842800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr15:45841600-45841800	Bivalent Enhancer	HepG2	liver
10	chr15:45841600-45841800	Active TSS	K562	blood
11	chr15:45841600-45842400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:45841600-45842400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:45841600-45842600	Enhancers	NHEK	skin
14	chr15:45841600-45842600	Enhancers	Osteobl	bone
15	chr15:45841600-45842800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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