Variant report

Variant	rs4897489
Chromosome Location	chr6:131371068-131371069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131370012..131372653-chr6:131373371..131376105,2	K562	blood:

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]
rs4895906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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]
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
rs4897489	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	chr6:131351400-131375000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:131351600-131374600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:131352400-131374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:131356600-131375000	Weak transcription	Brain Angular Gyrus	brain
6	chr6:131359000-131374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:131360800-131374800	Weak transcription	HSMM	muscle
8	chr6:131360800-131375000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:131361400-131373800	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:131363800-131371400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:131364000-131372200	Weak transcription	NHLF	lung
12	chr6:131364400-131372600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:131364400-131374600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:131367800-131374600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:131368000-131372600	Weak transcription	HepG2	liver
16	chr6:131368200-131374800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:131368200-131375200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:131369200-131372600	Weak transcription	Ovary	ovary
19	chr6:131369600-131372200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:131369600-131372400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:131369600-131372800	Enhancers	NHDF-Ad	bronchial
22	chr6:131370000-131371200	Enhancers	Brain Cingulate Gyrus	brain
23	chr6:131370000-131372200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:131370200-131371200	Enhancers	Fetal Stomach	stomach
25	chr6:131370400-131371200	Enhancers	Rectal Smooth Muscle	rectum
26	chr6:131370400-131372600	Enhancers	Osteobl	bone
27	chr6:131370400-131373600	Weak transcription	Fetal Lung	lung
28	chr6:131370400-131374600	Weak transcription	Brain Anterior Caudate	brain
29	chr6:131370600-131371800	Enhancers	Colon Smooth Muscle	Colon
30	chr6:131370600-131372400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:131370600-131374600	Weak transcription	A549	lung
32	chr6:131370800-131371200	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr6:131370800-131372400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:131371000-131371200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:131371000-131371200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr6:131371000-131371200	Enhancers	Psoas Muscle	Psoas
37	chr6:131371000-131374600	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:131371000-131375000	Weak transcription	Brain Substantia Nigra	brain

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