Variant report

Variant	rs4590017
Chromosome Location	chr4:85898741-85898742
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	chr4:85886329..85888550-chr4:85898152..85900463,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180769	Chromatin interaction
ENSG00000163625	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10856852	0.82[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs11097028	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11732309	0.80[EUR][1000 genomes]
rs11732347	0.80[EUR][1000 genomes]
rs12500519	0.84[EUR][1000 genomes]
rs12502559	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12503330	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13118671	0.93[ASW][hapmap];0.90[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs13125323	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13139541	0.93[EUR][1000 genomes]
rs13141072	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1484661	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs1508670	0.90[CEU][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17009317	0.86[ASW][hapmap];0.90[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs17009334	0.90[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs17009341	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs2046404	0.86[JPT][hapmap]
rs28754901	0.83[EUR][1000 genomes]
rs34314581	0.80[EUR][1000 genomes]
rs35190829	0.88[EUR][1000 genomes]
rs35892581	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383611	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4533765	0.84[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4626191	0.80[EUR][1000 genomes]
rs55871210	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55912355	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56094216	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56194765	0.80[EUR][1000 genomes]
rs58074983	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6531777	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs6531782	0.82[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs6531783	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66965560	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67624868	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6815917	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6820517	0.95[EUR][1000 genomes]
rs6829807	0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs6847564	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs71631375	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72664928	0.83[EUR][1000 genomes]
rs72664957	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7654035	0.86[JPT][hapmap]
rs7661609	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs7663580	0.82[CEU][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs7682896	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7690054	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7692223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7694949	0.86[JPT][hapmap];0.90[TSI][hapmap]
rs7695054	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7699226	0.86[JPT][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4590017	HERC5	cis	cerebellum	SCAN
rs4590017	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85888800-85908000	Weak transcription	Pancreas	Pancrea
2	chr4:85888800-85909400	Weak transcription	Brain Angular Gyrus	brain
3	chr4:85889000-85906000	Weak transcription	HSMM	muscle
4	chr4:85889000-85907800	Weak transcription	Brain Substantia Nigra	brain
5	chr4:85889000-85908200	Weak transcription	Aorta	Aorta
6	chr4:85889000-85908400	Weak transcription	Ovary	ovary
7	chr4:85889000-85909200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:85890400-85901600	Weak transcription	Adipose Nuclei	Adipose
9	chr4:85890400-85901800	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:85896600-85900200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr4:85898000-85899800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr4:85898200-85899000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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