Variant report

Variant	rs2088500
Chromosome Location	chr10:4687532-4687533
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:4681477..4684219-chr10:4687339..4690160,2	K562	blood:
2	chr10:3826834..3829522-chr10:4687271..4690305,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067082	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1025921	0.95[ASN][1000 genomes]
rs10444199	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10508286	0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs10795195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10904310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10904311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10904312	0.88[ASN][1000 genomes]
rs10904313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10904316	0.96[ASN][1000 genomes]
rs11252641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11252642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11252646	0.87[ASN][1000 genomes]
rs11252648	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs11252653	0.97[ASN][1000 genomes]
rs12780788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12782668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1838239	0.92[YRI][hapmap]
rs2083873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[ASN][1000 genomes]
rs2165955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2173368	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313453	0.83[AMR][1000 genomes];0.94[EUR][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	nsv894787	chr10:4385379-4857717	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv894791	chr10:4624233-4687532	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2563012	chr10:4686396-4688007	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv2384891	chr10:4686882-4687831	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3313552	chr10:4686954-4687743	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3313563	chr10:4686954-4687743	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:4680600-4694200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr10:4680600-4703800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:4680800-4692800	Weak transcription	Aorta	Aorta
4	chr10:4682800-4688800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:4682800-4690800	Weak transcription	Psoas Muscle	Psoas
6	chr10:4682800-4693800	Weak transcription	NHEK	skin
7	chr10:4682800-4694000	Weak transcription	HMEC	breast
8	chr10:4683800-4689000	Weak transcription	HUVEC	blood vessel
9	chr10:4684400-4692200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr10:4685800-4692600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr10:4686800-4689200	Weak transcription	Adipose Nuclei	Adipose

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