Variant report

Variant	rs11133403
Chromosome Location	chr4:56476113-56476114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56471770..56474121-chr4:56475653..56477265,2	K562	blood:
2	chr4:56465744..56469712-chr4:56475129..56477433,3	K562	blood:
3	chr4:56466882..56469712-chr4:56475375..56477433,2	K562	blood:
4	chr4:56474369..56476951-chr4:56481028..56484786,4	K562	blood:
5	chr4:56472621..56475219-chr4:56475225..56477153,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10462032	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1047354	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs10517344	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs10517346	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1056545	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1056547	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs10866425	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11133377	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs11133378	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs11133380	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs11133385	0.80[CHB][hapmap]
rs11133386	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs11133388	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs11133391	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs11133397	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs11133398	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs11133400	0.81[ASN][1000 genomes]
rs11935823	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs11942472	0.81[ASN][1000 genomes]
rs11943206	0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap]
rs11945489	0.93[ASN][1000 genomes]
rs12500686	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs12500837	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12500852	0.81[ASN][1000 genomes]
rs12501636	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs12504300	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12506788	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs12510400	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12510681	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs12644948	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs12648271	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs12649507	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs12649925	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651640	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs13108409	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs13113518	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs13114841	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs13116035	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs13116194	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs13120134	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs13122619	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs13124436	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs13132085	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13132420	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs13139100	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146987	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs13147861	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13149422	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13152173	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs1464490	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1522112	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs1522114	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1554483	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1586555	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2035691	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2087319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2171618	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs2272073	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs2279458	0.84[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap]
rs2412648	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs3749474	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs3805148	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3805150	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3805151	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs3805155	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs3805382	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3805384	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811826	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256282	0.81[ASN][1000 genomes]
rs4340844	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4864542	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs4864543	0.90[CHB][hapmap]
rs4864546	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs4864547	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4864548	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs4864996	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4864997	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4864999	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4865007	0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs4865011	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs6828570	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs6843722	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6849474	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7658446	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7660980	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7677085	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs7686261	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7690837	0.81[ASN][1000 genomes]
rs7691799	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs7696832	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9312661	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs939823	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs9790523	0.81[ASN][1000 genomes]

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	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv998179	chr4:56425126-56694339	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv932636	chr4:56438618-56667329	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11133403	SRD5A3-AS1	cis	Esophagus Mucosa	GTEx
rs11133403	SRD5A2L	Cis_1M	lymphoblastoid	RTeQTL
rs11133403	SRD5A3	cis	Esophagus Mucosa	GTEx
rs11133403	SRD5A2L	cis	multi-tissue	Pritchard
rs11133403	SRD5A3	cis	Whole Blood	GTEx
rs11133403	SRD5A3	cis	Artery Aorta	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56465400-56479400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:56469800-56481200	Weak transcription	Esophagus	oesophagus
3	chr4:56470400-56478800	Strong transcription	K562	blood
4	chr4:56472400-56476600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:56473600-56491600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr4:56474600-56477200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:56474800-56476200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr4:56474800-56476200	Enhancers	NHDF-Ad	bronchial
9	chr4:56474800-56476400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:56474800-56476400	Enhancers	HSMM	muscle
11	chr4:56475200-56476200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:56475200-56476400	Enhancers	Stomach Mucosa	stomach
13	chr4:56475400-56476200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:56475400-56476200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:56475600-56476200	Enhancers	Primary T cells from cord blood	blood
16	chr4:56475600-56476200	Active TSS	Thymus	Thymus
17	chr4:56475600-56476200	Enhancers	HSMMtube	muscle
18	chr4:56475600-56478200	Enhancers	Fetal Thymus	thymus
19	chr4:56475600-56479000	Enhancers	HMEC	breast
20	chr4:56475800-56476200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr4:56475800-56476200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:56475800-56476200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:56475800-56476200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:56475800-56476400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr4:56476000-56476200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr4:56476000-56476200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr4:56476000-56476400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:56476000-56476400	Flanking Active TSS	NHEK	skin

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