Variant report

Variant	rs17647588
Chromosome Location	chr2:178136077-178136078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178135429..178137464-chr2:178191123..178193752,2	K562	blood:
2	chr2:178074084..178077202-chr2:178131776..178136950,5	MCF-7	breast:
3	chr2:178134954..178137306-chr2:178146241..178147747,2	MCF-7	breast:
4	chr2:178133439..178136379-chr2:178282371..178284754,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10183914	0.96[CEU][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs13001694	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13005431	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13028464	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17524059	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17581525	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1806649	0.89[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs34468415	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34551701	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35284526	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35440573	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36030784	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62173695	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17647588	HOXD11	cis	cerebellum	SCAN
rs17647588	SP9	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178130400-178137600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:178131600-178136400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:178131600-178138200	Weak transcription	Fetal Lung	lung
4	chr2:178131600-178139400	Weak transcription	Fetal Stomach	stomach
5	chr2:178131600-178140400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:178131600-178154800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:178131800-178137000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:178131800-178137000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:178131800-178137000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:178131800-178137400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:178131800-178137600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:178131800-178137600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:178131800-178137600	Weak transcription	HUVEC	blood vessel
14	chr2:178131800-178137800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:178131800-178144600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:178131800-178146800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:178132000-178137600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:178132000-178139400	Weak transcription	Aorta	Aorta
19	chr2:178132000-178139600	Weak transcription	HSMM	muscle
20	chr2:178132000-178140000	Weak transcription	Ovary	ovary
21	chr2:178132400-178137600	Weak transcription	Primary T cells from cord blood	blood
22	chr2:178133400-178136400	Weak transcription	Hela-S3	cervix
23	chr2:178133400-178137000	Enhancers	A549	lung
24	chr2:178133800-178136800	Weak transcription	Fetal Intestine Large	intestine
25	chr2:178134000-178137600	Weak transcription	Liver	Liver
26	chr2:178134400-178136200	Weak transcription	HepG2	liver
27	chr2:178135000-178137600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:178135200-178137600	Weak transcription	Stomach Mucosa	stomach
29	chr2:178135400-178138000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:178135400-178138000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:178135400-178138000	Weak transcription	NH-A	brain
32	chr2:178135400-178139400	Weak transcription	HMEC	breast
33	chr2:178135400-178140400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:178135600-178137600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:178135800-178137000	Weak transcription	NHEK	skin
36	chr2:178136000-178136200	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links