Variant report

Variant	rs656163
Chromosome Location	chr11:58951440-58951441
allele	A/G
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	CEBPB	chr11:58951311-58951539	Hela-S3	cervix:	n/a	chr11:58951432-58951443 chr11:58951431-58951444
2	WRNIP1	chr11:58951339-58951483	GM12878	blood:	n/a	n/a
3	CEBPB	chr11:58951269-58951525	HepG2	liver:	n/a	chr11:58951432-58951443 chr11:58951431-58951444

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58938992..58941920-chr11:58950361..58952381,2	MCF-7	breast:
2	chr11:58939495..58941114-chr11:58948747..58951502,2	MCF-7	breast:

Variant related genes	Relation type
DTX4	TF binding region
ENSG00000110042	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1048444	0.89[YRI][hapmap]
rs11607278	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs2000478	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs2211912	0.92[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs3847	0.89[YRI][hapmap]
rs4939269	0.85[CEU][hapmap]
rs5029315	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs610123	0.89[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs6591509	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs7131079	0.81[CEU][hapmap]
rs7944135	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs656163	UBE2L6	cis	parietal	SCAN
rs656163	OR5B2	cis	parietal	SCAN
rs656163	MPEG1	Cis_1M	lymphoblastoid	RTeQTL
rs656163	DTX4	cis	Nerve Tibial	GTEx
rs656163	SNORD28	cis	cerebellum	SCAN
rs656163	DDB1	cis	cerebellum	SCAN
rs656163	DTX4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58941600-58964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:58942200-58951600	Weak transcription	Colon Smooth Muscle	Colon
3	chr11:58943400-58952600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:58943400-58954800	Weak transcription	Hela-S3	cervix
5	chr11:58943600-58975400	Weak transcription	NHEK	skin
6	chr11:58947200-58952800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:58947400-58953400	Weak transcription	HMEC	breast
8	chr11:58947600-58955000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr11:58948200-58951800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:58948400-58951600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:58948600-58952200	Genic enhancers	Rectal Mucosa Donor 29	rectum
12	chr11:58948600-58952600	Strong transcription	Primary B cells from cord blood	blood
13	chr11:58948600-58953600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr11:58949000-58951800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:58949000-58951800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
16	chr11:58949000-58952000	Genic enhancers	Duodenum Mucosa	Duodenum
17	chr11:58949000-58952800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:58949200-58951600	Strong transcription	Brain Germinal Matrix	brain
19	chr11:58949200-58951800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:58949200-58952400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:58949200-58952800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:58949400-58951600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:58949400-58951800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:58949400-58952800	Genic enhancers	Fetal Intestine Large	intestine
25	chr11:58949400-58973400	Weak transcription	Right Ventricle	heart
26	chr11:58949600-58952800	Genic enhancers	Fetal Intestine Small	intestine
27	chr11:58949600-58953000	Genic enhancers	Liver	Liver
28	chr11:58949800-58952000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:58949800-58952200	Genic enhancers	Rectal Mucosa Donor 31	rectum
30	chr11:58950000-58951600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:58950000-58951600	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr11:58950000-58952200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:58950200-58951800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr11:58950200-58951800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
36	chr11:58950200-58952000	Enhancers	Small Intestine	intestine
37	chr11:58950200-58952400	Genic enhancers	Fetal Stomach	stomach
38	chr11:58950200-58953400	Enhancers	Stomach Mucosa	stomach
39	chr11:58950200-58958600	Weak transcription	Aorta	Aorta
40	chr11:58950400-58951600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr11:58950400-58951600	Genic enhancers	Fetal Lung	lung
42	chr11:58950400-58951600	Weak transcription	Spleen	Spleen
43	chr11:58950400-58951800	Genic enhancers	Adipose Nuclei	Adipose
44	chr11:58950400-58952800	Weak transcription	HSMM	muscle
45	chr11:58950400-58953800	Enhancers	Brain Hippocampus Middle	brain
46	chr11:58950400-58957400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr11:58950400-58972200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:58950600-58951800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:58950600-58953600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr11:58950800-58951800	Genic enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links