Variant report

Variant	rs17113057
Chromosome Location	chr1:85101762-85101763
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85094796..85097662-chr1:85099991..85101818,2	K562	blood:

Variant related genes	Relation type
ENSG00000180869	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11164027	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11164029	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164030	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164043	0.84[GIH][hapmap]
rs12025014	0.81[CEU][hapmap]
rs12031476	0.80[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12035493	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs12042947	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs12045905	0.82[AMR][1000 genomes]
rs17113051	0.90[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2911568	1.00[JPT][hapmap]
rs2911613	0.89[GIH][hapmap]
rs6659803	0.82[AMR][1000 genomes]
rs6686971	0.81[CEU][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap]
rs6695249	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7536572	0.81[CEU][hapmap];0.87[GIH][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs818521	0.85[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17113057	SPATA1	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85087000-85147400	Weak transcription	Gastric	stomach
2	chr1:85098400-85101800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:85099000-85109600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:85099000-85115600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:85099000-85123400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:85099200-85109200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:85099200-85109800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:85099200-85115000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:85099200-85121400	Weak transcription	NHDF-Ad	bronchial
10	chr1:85099200-85138200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:85099400-85105600	Weak transcription	K562	blood
12	chr1:85099400-85115000	Weak transcription	Osteobl	bone
13	chr1:85099400-85131200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:85099600-85122600	Weak transcription	Fetal Brain Male	brain
15	chr1:85100200-85106200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:85100600-85112400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:85100600-85116800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:85101000-85103000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:85101000-85123200	Weak transcription	Fetal Kidney	kidney
20	chr1:85101000-85124400	Weak transcription	Hela-S3	cervix
21	chr1:85101200-85105800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:85101400-85105600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:85101400-85109000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:85101600-85101800	Weak transcription	Fetal Intestine Small	intestine
25	chr1:85101600-85102600	Weak transcription	HMEC	breast
26	chr1:85101600-85105800	Weak transcription	Fetal Intestine Large	intestine
27	chr1:85101600-85121000	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links