Variant report

Variant	rs4895906
Chromosome Location	chr6:131358672-131358673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131356533..131360824-chr6:131360872..131363958,3	MCF-7	breast:
2	chr6:131356781..131360402-chr6:131360756..131363630,4	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12525104	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525986	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13437326	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17178878	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17179123	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17180687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17180867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17784418	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17784472	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17784896	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17785507	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1811949	0.89[ASN][1000 genomes]
rs1977576	0.95[ASN][1000 genomes]
rs2297853	0.89[ASN][1000 genomes]
rs28482889	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34899420	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4895901	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4895903	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895904	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897478	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897483	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897484	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897485	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897486	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897491	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4897492	0.85[AMR][1000 genomes]
rs4897496	0.80[AFR][1000 genomes]
rs55898152	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56163502	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56173113	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56201801	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58503799	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62422362	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62422365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62422380	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62423581	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62423597	0.95[EUR][1000 genomes]
rs62423598	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6906059	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6916024	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921396	0.89[ASN][1000 genomes]
rs6922045	0.89[ASN][1000 genomes]
rs6928920	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741148	0.89[ASN][1000 genomes]
rs7755720	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7758016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769678	0.89[ASN][1000 genomes]
rs7771543	0.89[ASN][1000 genomes]
rs9385568	0.89[ASN][1000 genomes]
rs9402303	0.89[ASN][1000 genomes]
rs9483206	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954211	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[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
rs4895906	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131346000-131375000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:131349000-131358800	Weak transcription	Pancreas	Pancrea
3	chr6:131351400-131359800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:131351400-131360200	Weak transcription	Small Intestine	intestine
5	chr6:131351400-131361400	Weak transcription	Psoas Muscle	Psoas
6	chr6:131351400-131375000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:131351600-131359400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:131351600-131359400	Weak transcription	Fetal Lung	lung
9	chr6:131351600-131360200	Weak transcription	Fetal Stomach	stomach
10	chr6:131351600-131374600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:131351800-131360000	Weak transcription	A549	lung
12	chr6:131352000-131359400	Weak transcription	HSMM	muscle
13	chr6:131352000-131360000	Weak transcription	NH-A	brain
14	chr6:131352200-131358800	Weak transcription	Lung	lung
15	chr6:131352200-131359400	Weak transcription	NHLF	lung
16	chr6:131352200-131359800	Weak transcription	Brain Substantia Nigra	brain
17	chr6:131352200-131360200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:131352200-131360200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:131352400-131374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:131353800-131359800	Enhancers	HepG2	liver
21	chr6:131353800-131364000	Weak transcription	Ovary	ovary
22	chr6:131355200-131358800	Weak transcription	Aorta	Aorta
23	chr6:131356200-131359000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr6:131356600-131375000	Weak transcription	Brain Angular Gyrus	brain
25	chr6:131357200-131360000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:131357400-131367200	Weak transcription	Fetal Intestine Small	intestine
27	chr6:131358000-131358800	Weak transcription	NHDF-Ad	bronchial
28	chr6:131358000-131360000	Enhancers	Osteobl	bone
29	chr6:131358200-131359800	Weak transcription	Brain Anterior Caudate	brain
30	chr6:131358200-131359800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:131358200-131360200	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:131358400-131359400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:131358400-131359800	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:131358400-131359800	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:131358600-131358800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:131358600-131359000	Enhancers	Left Ventricle	heart
37	chr6:131358600-131359600	Weak transcription	Adipose Nuclei	Adipose
38	chr6:131358600-131360800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links