Variant report

Variant	rs17059954
Chromosome Location	chr6:131334473-131334474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10872375	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11154611	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11760051	0.93[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12195366	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12196734	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12197829	0.93[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12203760	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12214021	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1569195	0.88[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1976981	0.89[ASN][1000 genomes]
rs2151068	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2178282	0.90[ASN][1000 genomes]
rs28812545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4259270	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4498389	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs62423583	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6901548	0.88[ASN][1000 genomes]
rs6902930	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6903705	0.90[ASN][1000 genomes]
rs6905151	0.93[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6907809	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6916206	0.93[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs6921542	0.90[ASN][1000 genomes]
rs6926372	0.88[ASN][1000 genomes]
rs7763960	0.89[ASN][1000 genomes]
rs7770892	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9321264	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9372986	0.99[ASN][1000 genomes]
rs9372987	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9372989	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9375784	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9375785	0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9375787	0.93[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9375788	0.93[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9375789	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9375790	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375794	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs9375795	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375796	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9375797	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9388873	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9388876	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9388880	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9398967	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9398969	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9398970	0.90[ASN][1000 genomes]
rs9398971	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9398972	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9398973	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9398975	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9398976	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9402306	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs9402310	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402313	0.90[ASN][1000 genomes]
rs9402314	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9483210	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9492790	0.87[ASN][1000 genomes]
rs9492792	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs951251	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs954919	0.88[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17059954	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131328400-131334800	Weak transcription	A549	lung
2	chr6:131329800-131334600	Weak transcription	Fetal Stomach	stomach
3	chr6:131329800-131334800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:131329800-131334800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:131329800-131336400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:131329800-131347400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:131330000-131335000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:131330000-131335000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:131330200-131334800	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:131330200-131335400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:131330400-131336400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:131330800-131334600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:131331200-131334800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:131331400-131334800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:131332200-131334600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:131332200-131345400	Weak transcription	Left Ventricle	heart
17	chr6:131332400-131334800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:131332800-131334600	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:131332800-131339600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:131333000-131334800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:131333400-131335400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:131333600-131334800	Enhancers	Brain Anterior Caudate	brain
23	chr6:131333600-131339200	Weak transcription	Pancreas	Pancrea
24	chr6:131333800-131334600	Enhancers	Adipose Nuclei	Adipose
25	chr6:131333800-131334600	Enhancers	Fetal Lung	lung
26	chr6:131333800-131334600	Enhancers	HUVEC	blood vessel
27	chr6:131333800-131334800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:131333800-131334800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr6:131333800-131335000	Enhancers	HSMMtube	muscle
30	chr6:131333800-131337400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr6:131334000-131334600	Enhancers	HSMM	muscle
32	chr6:131334000-131337000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:131334000-131337400	Enhancers	Fetal Kidney	kidney
34	chr6:131334200-131334800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:131334200-131334800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr6:131334200-131334800	Enhancers	NHDF-Ad	bronchial
37	chr6:131334200-131334800	Enhancers	NHLF	lung
38	chr6:131334400-131334600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:131334400-131334600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:131334400-131334600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:131334400-131334600	Enhancers	Brain Angular Gyrus	brain
42	chr6:131334400-131335200	Active TSS	Ovary	ovary
43	chr6:131334400-131335400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr6:131334400-131335400	Enhancers	NH-A	brain
45	chr6:131334400-131335800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:131334400-131337200	Weak transcription	Small Intestine	intestine
47	chr6:131334400-131337400	Enhancers	HMEC	breast

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