Variant report

Variant	rs9398969
Chromosome Location	chr6:131354491-131354492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10872375	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11154611	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11760051	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195366	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12196734	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12197829	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203760	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12214021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1569195	0.96[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17059954	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]
rs1976981	0.98[ASN][1000 genomes]
rs2151068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178282	0.99[ASN][1000 genomes]
rs28812545	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259270	0.89[CEU][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]
rs4498389	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs62423583	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6901548	0.97[ASN][1000 genomes]
rs6902930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903705	0.99[ASN][1000 genomes]
rs6905151	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs6907809	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6916206	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6921542	0.99[ASN][1000 genomes]
rs6926372	0.97[ASN][1000 genomes]
rs7763960	0.98[ASN][1000 genomes]
rs7770892	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9321264	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9372986	0.91[ASN][1000 genomes]
rs9372987	1.00[CEU][hapmap];1.00[CHB][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]
rs9372989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9375784	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9375785	0.80[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375787	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9375788	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9375789	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375790	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9375794	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9375795	0.91[CEU][hapmap];0.93[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]
rs9375796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375797	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs9388873	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9388876	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388880	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9398967	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398970	0.99[ASN][1000 genomes]
rs9398971	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9398972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398973	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398975	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9398976	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9402301	0.85[ASN][1000 genomes]
rs9402306	0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs9402310	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9402313	0.99[ASN][1000 genomes]
rs9402314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483210	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9492790	0.95[ASN][1000 genomes]
rs9492792	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs951251	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs954919	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[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
rs9398969	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131345800-131357600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:131346000-131375000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:131349000-131358800	Weak transcription	Pancreas	Pancrea
4	chr6:131351400-131356200	Weak transcription	Brain Angular Gyrus	brain
5	chr6:131351400-131356200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:131351400-131356400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:131351400-131356400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:131351400-131356800	Weak transcription	Fetal Intestine Small	intestine
9	chr6:131351400-131357400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:131351400-131359800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:131351400-131360200	Weak transcription	Small Intestine	intestine
12	chr6:131351400-131361400	Weak transcription	Psoas Muscle	Psoas
13	chr6:131351400-131375000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:131351600-131355200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:131351600-131356200	Weak transcription	Fetal Intestine Large	intestine
16	chr6:131351600-131356400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:131351600-131357400	Weak transcription	Adipose Nuclei	Adipose
18	chr6:131351600-131357800	Weak transcription	Colon Smooth Muscle	Colon
19	chr6:131351600-131358000	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:131351600-131358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:131351600-131359400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:131351600-131359400	Weak transcription	Fetal Lung	lung
23	chr6:131351600-131360200	Weak transcription	Fetal Stomach	stomach
24	chr6:131351600-131374600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:131351800-131360000	Weak transcription	A549	lung
26	chr6:131352000-131357600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:131352000-131358000	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:131352000-131359400	Weak transcription	HSMM	muscle
29	chr6:131352000-131360000	Weak transcription	NH-A	brain
30	chr6:131352200-131357800	Weak transcription	NHDF-Ad	bronchial
31	chr6:131352200-131358800	Weak transcription	Lung	lung
32	chr6:131352200-131359400	Weak transcription	NHLF	lung
33	chr6:131352200-131359800	Weak transcription	Brain Substantia Nigra	brain
34	chr6:131352200-131360200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:131352200-131360200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:131352400-131374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:131353200-131357800	Weak transcription	Brain Anterior Caudate	brain
38	chr6:131353800-131359800	Enhancers	HepG2	liver
39	chr6:131353800-131364000	Weak transcription	Ovary	ovary
40	chr6:131354400-131354600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:131354400-131354600	Enhancers	Aorta	Aorta
42	chr6:131354400-131354600	Enhancers	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links