Variant report

Variant	rs10087958
Chromosome Location	chr8:52866669-52866670
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	chr8:52860319..52862626-chr8:52865523..52867110,2	MCF-7	breast:
2	chr8:52810400..52813872-chr8:52865354..52871657,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168300	Chromatin interaction
ENSG00000228801	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10453128	0.82[ASN][1000 genomes]
rs10504130	0.82[JPT][hapmap]
rs10958305	0.82[JPT][hapmap]
rs11775587	0.82[JPT][hapmap]
rs11775611	0.82[JPT][hapmap]
rs11781330	0.85[JPT][hapmap]
rs11785805	0.82[JPT][hapmap]
rs12541693	0.88[JPT][hapmap]
rs12544872	0.81[JPT][hapmap]
rs12546159	0.87[JPT][hapmap]
rs1515688	0.84[EUR][1000 genomes]
rs1589079	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16916856	0.82[JPT][hapmap]
rs16916865	0.82[JPT][hapmap]
rs16916966	0.87[CEU][hapmap];0.94[CHB][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16916968	0.81[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17284746	0.82[JPT][hapmap]
rs2138297	1.00[ASN][1000 genomes]
rs2176119	1.00[ASN][1000 genomes]
rs41453644	0.82[JPT][hapmap]
rs6473666	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6768	0.81[JPT][hapmap]
rs6993367	0.83[EUR][1000 genomes]
rs6994203	0.82[JPT][hapmap]
rs7001651	0.82[EUR][1000 genomes]
rs7813414	0.92[ASN][1000 genomes]
rs7816834	0.81[ASN][1000 genomes]
rs7817558	0.82[ASN][1000 genomes]
rs7817892	0.82[ASN][1000 genomes]
rs7819892	0.90[ASN][1000 genomes]
rs7820177	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7833668	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.90[ASN][1000 genomes]
rs7834181	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs7838307	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs7843189	0.83[EUR][1000 genomes]
rs877248	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10087958	PCMTD1	cis	cerebellum	SCAN
rs10087958	C11orf63	trans	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52850200-52868000	Weak transcription	Primary B cells from cord blood	blood
2	chr8:52852000-52870000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr8:52852600-52867600	Weak transcription	Fetal Kidney	kidney
4	chr8:52852800-52867000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:52861200-52870000	Weak transcription	Fetal Muscle Leg	muscle
6	chr8:52866400-52867400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr8:52866600-52867800	Enhancers	Primary B cells from peripheral blood	blood
8	chr8:52866600-52867800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr8:52866600-52868000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr8:52866600-52868000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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