Variant report

Variant	rs2059795
Chromosome Location	chr5:111538506-111538507
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	RUNX3	chr5:111538454-111538732	GM12878	blood:	n/a	n/a
2	EBF1	chr5:111538419-111538619	GM12878	blood:	n/a	n/a
3	FOS	chr5:111538423-111538805	MCF10A-Er-Src	breast:	n/a	n/a
4	NFIC	chr5:111538417-111538728	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000251187	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10051634	0.81[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1109590	0.91[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11740779	0.88[ASN][1000 genomes]
rs11746754	0.88[ASN][1000 genomes]
rs12518022	0.81[MEX][hapmap]
rs12659409	0.82[ASN][1000 genomes]
rs13158835	0.81[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs13165201	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs13176696	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1366143	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs17134212	0.86[ASN][1000 genomes]
rs2288396	0.83[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs34832895	0.87[ASN][1000 genomes]
rs4957635	0.83[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4958006	0.83[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6873658	0.87[ASN][1000 genomes]
rs6884477	0.81[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7712166	0.92[ASN][1000 genomes]
rs7722065	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2059795	WDR36	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111497600-111538600	Weak transcription	Small Intestine	intestine
2	chr5:111501400-111546400	Weak transcription	Spleen	Spleen
3	chr5:111502400-111546400	Weak transcription	Aorta	Aorta
4	chr5:111502800-111546000	Weak transcription	Ovary	ovary
5	chr5:111504800-111541400	Weak transcription	Right Ventricle	heart
6	chr5:111504800-111557800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:111504800-111586400	Weak transcription	Gastric	stomach
8	chr5:111505600-111541800	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:111510800-111540000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:111510800-111547400	Weak transcription	HUVEC	blood vessel
11	chr5:111519000-111546400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:111519200-111553800	Weak transcription	Pancreas	Pancrea
13	chr5:111519800-111553600	Weak transcription	Esophagus	oesophagus
14	chr5:111523400-111540600	Weak transcription	Hela-S3	cervix
15	chr5:111529800-111553600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:111535000-111541800	Weak transcription	Fetal Brain Female	brain
17	chr5:111535200-111538800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:111535600-111539400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:111535600-111540200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:111536000-111538800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:111536200-111538600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:111536400-111538800	Strong transcription	Adipose Nuclei	Adipose
23	chr5:111536400-111539000	Weak transcription	Fetal Lung	lung
24	chr5:111536400-111541600	Weak transcription	Fetal Stomach	stomach
25	chr5:111536600-111540600	Strong transcription	Placenta	Placenta
26	chr5:111536800-111539000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:111537200-111540000	Weak transcription	Fetal Heart	heart
28	chr5:111537400-111538600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:111537400-111538600	Strong transcription	Lung	lung
30	chr5:111537400-111538800	Strong transcription	Left Ventricle	heart
31	chr5:111537400-111539000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:111537800-111538600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr5:111537800-111538600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:111537800-111538600	Strong transcription	Fetal Kidney	kidney
35	chr5:111537800-111539200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:111537800-111539400	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr5:111538000-111538600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:111538000-111541800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr5:111538000-111553400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr5:111538200-111539600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr5:111538200-111540000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:111538200-111543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:111538200-111546400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:111538400-111538800	Enhancers	NHEK	skin
45	chr5:111538400-111540000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:111538400-111540000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:111538400-111540800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links