Variant report

Variant	rs954211
Chromosome Location	chr6:131373431-131373432
allele	A/T
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: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs12525104	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12525986	0.88[EUR][1000 genomes]
rs13437326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17178878	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17179123	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17180687	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17180867	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17770255	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs17784418	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17784472	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17784896	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17785507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1811949	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2095961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2183967	0.88[CEU][hapmap]
rs2297853	1.00[JPT][hapmap]
rs28482889	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];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34899420	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3777434	0.88[CEU][hapmap]
rs3777435	0.88[CEU][hapmap]
rs3777436	0.88[CEU][hapmap]
rs45550834	0.89[ASN][1000 genomes]
rs4895901	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4895903	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4895904	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4895906	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4895907	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4895908	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4895909	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897473	0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs4897478	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4897483	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897484	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897486	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897487	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897489	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897491	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4897492	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55898152	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56163502	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56173113	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56201801	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58503799	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62422362	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62422365	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62422380	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62423581	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62423597	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62423598	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6569707	0.88[CEU][hapmap]
rs6569708	0.84[CEU][hapmap]
rs6906059	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6906478	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]
rs6910656	0.91[ASN][1000 genomes]
rs6916024	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
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];0.91[ASN][1000 genomes]
rs6926250	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs6928920	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6931804	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6935108	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7741148	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7755720	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7758016	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7761311	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7769678	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7775013	0.88[CEU][hapmap]
rs9321263	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9372985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9385568	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9388861	0.90[CEU][hapmap]
rs9388863	0.88[CEU][hapmap]
rs9388872	0.91[ASN][1000 genomes]
rs9483206	1.00[JPT][hapmap];0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs954211	EPB41L2	cis	parietal	SCAN
rs954211	PSMD3	trans	cerebellum	SCAN

Chromatin state (count:37 , 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	chr6:131364400-131374600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:131367800-131374600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:131368200-131374800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:131368200-131375200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:131370400-131373600	Weak transcription	Fetal Lung	lung
15	chr6:131370400-131374600	Weak transcription	Brain Anterior Caudate	brain
16	chr6:131370600-131374600	Weak transcription	A549	lung
17	chr6:131371000-131374600	Weak transcription	Brain Hippocampus Middle	brain
18	chr6:131371000-131375000	Weak transcription	Brain Substantia Nigra	brain
19	chr6:131371200-131374200	Weak transcription	Fetal Stomach	stomach
20	chr6:131371200-131374600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:131371200-131374800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:131371200-131374800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:131371800-131375000	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:131372200-131373600	Weak transcription	NHEK	skin
25	chr6:131372200-131374000	Enhancers	NHLF	lung
26	chr6:131372200-131374600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:131372200-131375000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:131372400-131374600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:131372400-131374600	Weak transcription	HUVEC	blood vessel
30	chr6:131372600-131374000	Enhancers	HepG2	liver
31	chr6:131372600-131374800	Weak transcription	Adipose Nuclei	Adipose
32	chr6:131372600-131374800	Weak transcription	Osteobl	bone
33	chr6:131372800-131374600	Weak transcription	NHDF-Ad	bronchial
34	chr6:131373000-131374400	Weak transcription	HMEC	breast
35	chr6:131373400-131374000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:131373400-131374800	Weak transcription	Ovary	ovary
37	chr6:131373400-131381400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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