Variant report

Variant	rs6906478
Chromosome Location	chr6:131345133-131345134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs12525104	0.95[EUR][1000 genomes]
rs12525986	0.89[EUR][1000 genomes]
rs13437326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17178878	0.92[EUR][1000 genomes]
rs17179123	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17180687	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17180867	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17770255	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs17784418	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs17784472	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17784896	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17785507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1811949	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2095961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2183967	0.88[CEU][hapmap]
rs2297853	1.00[JPT][hapmap]
rs28482889	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34899420	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3777434	0.88[CEU][hapmap]
rs3777435	0.88[CEU][hapmap]
rs3777436	0.88[CEU][hapmap]
rs45550834	0.81[ASN][1000 genomes]
rs4895901	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs4895903	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4895904	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4895906	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4895907	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4895908	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4895909	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4897468	0.84[CEU][hapmap]
rs4897473	0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs4897478	0.92[EUR][1000 genomes]
rs4897483	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4897484	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4897485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4897486	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4897487	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4897489	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4897492	0.85[ASN][1000 genomes]
rs56163502	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56173113	0.89[EUR][1000 genomes]
rs56201801	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58503799	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62422362	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62422365	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62422380	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62423581	0.89[EUR][1000 genomes]
rs62423597	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62423598	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6569707	0.88[CEU][hapmap]
rs6569708	0.85[CEU][hapmap]
rs6906059	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6910656	0.83[ASN][1000 genomes]
rs6916024	0.97[EUR][1000 genomes]
rs6919007	0.85[CEU][hapmap]
rs6921396	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6922045	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6922177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6926250	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs6928920	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6931804	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6935108	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7741148	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7755720	0.89[EUR][1000 genomes]
rs7758016	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7760965	0.84[CEU][hapmap]
rs7761311	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7769678	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7775013	0.88[CEU][hapmap]
rs872576	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9321263	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9372985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9385568	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9388861	0.90[CEU][hapmap]
rs9388863	0.88[CEU][hapmap]
rs9388872	0.83[ASN][1000 genomes]
rs9402292	0.81[CEU][hapmap]
rs942	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9483206	1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs954211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6906478	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL
rs6906478	PSMD3	trans	cerebellum	SCAN
rs6906478	EPB41L2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131329800-131347400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:131332200-131345400	Weak transcription	Left Ventricle	heart
3	chr6:131335600-131345200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:131336600-131345200	Weak transcription	Ovary	ovary
5	chr6:131337400-131347200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:131337600-131345200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:131337800-131345200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:131337800-131345400	Weak transcription	Right Atrium	heart
9	chr6:131337800-131351000	Weak transcription	Stomach Mucosa	stomach
10	chr6:131338000-131345200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:131338200-131345200	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:131338200-131345200	Weak transcription	HepG2	liver
13	chr6:131339400-131349400	Weak transcription	Brain Angular Gyrus	brain
14	chr6:131341800-131345200	Weak transcription	Brain Substantia Nigra	brain
15	chr6:131343600-131345200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:131343600-131345400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:131344200-131345400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:131344400-131347600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:131345000-131345200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:131345000-131345200	Active TSS	Hela-S3	cervix
21	chr6:131345000-131345400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:131345000-131345400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:131345000-131345600	Flanking Active TSS	HMEC	breast
24	chr6:131345000-131345600	Flanking Active TSS	NHDF-Ad	bronchial
25	chr6:131345000-131345800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:131345000-131345800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr6:131345000-131345800	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr6:131345000-131345800	Enhancers	HSMM	muscle
29	chr6:131345000-131345800	Enhancers	HSMMtube	muscle
30	chr6:131345000-131345800	Flanking Active TSS	NHEK	skin
31	chr6:131345000-131346000	Enhancers	A549	lung
32	chr6:131345000-131346000	Enhancers	HUVEC	blood vessel
33	chr6:131345000-131346000	Enhancers	Osteobl	bone
34	chr6:131345000-131347000	Enhancers	NHLF	lung
35	chr6:131345000-131348000	Enhancers	Brain Anterior Caudate	brain
36	chr6:131345000-131348800	Enhancers	Brain Hippocampus Middle	brain

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