Variant report

Variant	rs11804125
Chromosome Location	chr1:165256640-165256641
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165253102..165255836-chr1:165256006..165257807,2	MCF-7	breast:
2	chr1:165127148..165129651-chr1:165256617..165259392,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11799765	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11808645	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs11809085	0.96[EUR][1000 genomes]
rs12138441	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs16842354	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs17405214	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6666930	1.00[CEU][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs6691412	1.00[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs6692353	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73013466	0.82[EUR][1000 genomes]
rs74118549	0.96[EUR][1000 genomes]
rs7537922	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][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	nsv869712	chr1:164866810-165299085	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11804125	B4GALT3	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165253600-165258200	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr1:165254600-165258800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:165254800-165257200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:165254800-165258800	Enhancers	Liver	Liver
5	chr1:165255600-165258200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr1:165256000-165258000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:165256400-165257600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:165256400-165257600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:165256400-165258000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr1:165256400-165258000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:165256400-165258000	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr1:165256400-165258200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:165256400-165258200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:165256600-165256800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:165256600-165256800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:165256600-165256800	Bivalent Enhancer	NHEK	skin
17	chr1:165256600-165257000	Enhancers	Fetal Intestine Small	intestine
18	chr1:165256600-165257000	Enhancers	HMEC	breast
19	chr1:165256600-165257200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:165256600-165258000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr1:165256600-165258000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:165256600-165258000	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links