Variant report

Variant	rs985572
Chromosome Location	chr11:17501751-17501752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1055574	0.81[JPT][hapmap]
rs1055577	0.81[JPT][hapmap]
rs1055581	0.81[JPT][hapmap]
rs10832792	0.89[EUR][1000 genomes]
rs2072225	0.86[GIH][hapmap];0.81[JPT][hapmap]
rs3758953	1.00[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs4757522	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6486371	0.88[EUR][1000 genomes]
rs7943395	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs985572	HPS5	cis	cerebellum	SCAN
rs985572	PRPH	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17498800-17502000	Enhancers	Dnd41	blood
2	chr11:17500600-17501800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:17500600-17502000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
4	chr11:17500800-17502000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:17501200-17501800	Enhancers	H9 Cell Line	embryonic stem cell
6	chr11:17501200-17502000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr11:17501400-17501800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
8	chr11:17501400-17501800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
9	chr11:17501400-17501800	Enhancers	Brain Substantia Nigra	brain
10	chr11:17501600-17501800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr11:17501600-17501800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr11:17501600-17501800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr11:17501600-17501800	Enhancers	Brain Cingulate Gyrus	brain
14	chr11:17501600-17503800	Weak transcription	Pancreas	Pancrea
15	chr11:17501600-17505800	Weak transcription	Fetal Intestine Small	intestine
16	chr11:17501600-17506200	Weak transcription	Fetal Intestine Large	intestine
17	chr11:17501600-17507600	Weak transcription	Gastric	stomach

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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