Variant report

Variant	rs10010528
Chromosome Location	chr4:147258509-147258510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:147165326..147167236-chr4:147257804..147260774,3	MCF-7	breast:
2	chr4:147250783..147254830-chr4:147255041..147259510,7	MCF-7	breast:
3	chr4:146856345..146860229-chr4:147256179..147259928,4	MCF-7	breast:
4	chr4:147162002..147168172-chr4:147253902..147262824,27	MCF-7	breast:
5	chr4:147162568..147164848-chr4:147257539..147260414,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251010	Chromatin interaction
ENSG00000151612	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10008275	0.90[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs10013722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020390	0.86[JPT][hapmap]
rs10027135	1.00[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10027855	0.87[ASW][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap]
rs10032088	0.90[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11100924	0.92[CHD][hapmap];0.85[MEX][hapmap]
rs11725876	0.92[CHD][hapmap];0.85[MEX][hapmap]
rs11735261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11736003	0.94[ASN][1000 genomes]
rs11737121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11939345	0.92[ASN][1000 genomes]
rs11947781	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs17021396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2200474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2679141	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs28521842	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28625764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3849035	0.92[CHD][hapmap];0.85[MEX][hapmap]
rs4835033	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[ASN][1000 genomes]
rs4835292	0.86[ASN][1000 genomes]
rs4835294	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4835296	0.98[ASN][1000 genomes]
rs4835297	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4835299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs55798872	0.94[ASN][1000 genomes]
rs57713263	0.94[ASN][1000 genomes]
rs6841790	0.86[JPT][hapmap]
rs6843145	0.92[CHD][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap]
rs6846294	0.92[ASN][1000 genomes]
rs6846584	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs6846846	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857911	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[ASN][1000 genomes]
rs6858794	0.92[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs9784436	0.80[ASN][1000 genomes]
rs9784437	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs9996311	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9999381	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][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	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3451660	chr4:147225135-147271246	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3443192	chr4:147225234-147271217	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3468025	chr4:147225279-147271172	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3468026	chr4:147225279-147271172	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1033640	chr4:147232217-147531881	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10010528	GYPA	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147212800-147264200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:147241800-147284800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:147255400-147258800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:147255400-147264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:147256000-147258600	Enhancers	Fetal Lung	lung
6	chr4:147256000-147258600	Enhancers	Hela-S3	cervix
7	chr4:147256000-147261400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:147256400-147258600	Enhancers	Liver	Liver
9	chr4:147256400-147258600	Enhancers	HUVEC	blood vessel
10	chr4:147257000-147259400	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr4:147257400-147258600	Enhancers	Ovary	ovary
12	chr4:147257400-147260000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:147257800-147261800	Weak transcription	HMEC	breast
14	chr4:147258000-147258600	Enhancers	A549	lung
15	chr4:147258400-147258600	Enhancers	Left Ventricle	heart
16	chr4:147258400-147258600	Enhancers	Lung	lung
17	chr4:147258400-147258600	Enhancers	GM12878-XiMat	blood

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