Variant report

Variant	rs1149606
Chromosome Location	chr11:76490058-76490059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr11:76489696-76490208	H1-hESC	embryonic stem cell:	n/a	chr11:76489897-76489904 chr11:76489897-76489904 chr11:76489897-76489904
2	POLR2A	chr11:76489683-76490109	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr11:76490000-76490150	AG10803	skin:	n/a	n/a
4	E2F6	chr11:76489752-76490125	H1-hESC	embryonic stem cell:	n/a	chr11:76489897-76489904 chr11:76489897-76489904 chr11:76489897-76489904

No.	Distal block	Cell Line	Cell type
1	chr11:76489897..76492683-chr11:76518337..76520113,2	MCF-7	breast:
2	chr11:76487745..76490433-chr22:18912039..18914397,2	MCF-7	breast:
3	chr11:76448469..76450791-chr11:76488926..76490777,2	K562	blood:

Variant related genes	Relation type
TSKU	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1149596	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1149597	0.83[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1149599	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1149605	0.84[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1149608	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1149609	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1149610	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1149612	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1149614	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1149615	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1149616	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs1149617	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1149618	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs1149619	0.91[EUR][1000 genomes]
rs1224955	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1664081	0.81[ASN][1000 genomes]
rs34909318	1.00[EUR][1000 genomes]
rs3740776	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3740777	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs881930	0.83[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[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	nsv897931	chr11:76489673-76540708	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1149606	RP11-21L23.3	cis	Adipose Subcutaneous	GTEx
rs1149606	GUCY2EP	cis	Thyroid	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76482800-76492400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:76485600-76492200	Weak transcription	Ovary	ovary
3	chr11:76486000-76492200	Weak transcription	Liver	Liver
4	chr11:76486400-76491600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr11:76487200-76491400	ZNF genes & repeats	A549	lung
6	chr11:76487800-76492200	Weak transcription	NHEK	skin
7	chr11:76488000-76492200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:76488400-76492000	Enhancers	Adipose Nuclei	Adipose
9	chr11:76488400-76493400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr11:76488600-76492200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:76488800-76492000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:76489000-76490200	Enhancers	Fetal Stomach	stomach
13	chr11:76489000-76491000	Weak transcription	HepG2	liver
14	chr11:76489200-76490800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr11:76489200-76491600	Weak transcription	Fetal Intestine Small	intestine
16	chr11:76489200-76491800	Weak transcription	HMEC	breast
17	chr11:76489400-76490200	Enhancers	Fetal Muscle Leg	muscle
18	chr11:76489400-76490400	Enhancers	HSMMtube	muscle
19	chr11:76489600-76490200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:76489600-76490200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:76489600-76491600	Weak transcription	Fetal Lung	lung
22	chr11:76489800-76491000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:76490000-76490200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:76490000-76490200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
25	chr11:76490000-76490600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
26	chr11:76490000-76490800	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links