Variant report

Variant	rs4259270
Chromosome Location	chr6:131365099-131365100
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	chr6:131363706..131366230-chr6:131367411..131369715,2	K562	blood:

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	1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195366	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12196734	0.88[CEU][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	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203760	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	0.99[ASN][1000 genomes]
rs17059954	0.88[CEU][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	0.89[CEU][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]
rs4498389	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	0.98[ASN][1000 genomes]
rs6907809	0.91[ASN][1000 genomes]
rs6916206	0.94[ASN][1000 genomes]
rs6921542	0.99[ASN][1000 genomes]
rs6926372	0.97[ASN][1000 genomes]
rs7763960	0.98[ASN][1000 genomes]
rs7770892	0.99[ASN][1000 genomes]
rs9321264	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9372986	0.91[ASN][1000 genomes]
rs9372987	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]
rs9372989	0.89[CEU][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	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375787	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9375788	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9375789	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375790	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9375794	0.98[ASN][1000 genomes]
rs9375795	0.86[CEU][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	0.89[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375797	0.99[ASN][1000 genomes]
rs9388873	0.89[CEU][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	0.89[CEU][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	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398969	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]
rs9398970	0.99[ASN][1000 genomes]
rs9398971	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	0.86[ASN][1000 genomes]
rs9402310	1.00[CEU][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	0.97[ASN][1000 genomes]
rs9492790	0.95[ASN][1000 genomes]
rs9492792	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	0.99[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
rs4259270	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 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	chr6:131357400-131367200	Weak transcription	Fetal Intestine Small	intestine
7	chr6:131359000-131374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:131360400-131365600	Weak transcription	Adipose Nuclei	Adipose
9	chr6:131360400-131367400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:131360600-131367200	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:131360800-131368000	Weak transcription	Small Intestine	intestine
12	chr6:131360800-131370000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:131360800-131374800	Weak transcription	HSMM	muscle
14	chr6:131360800-131375000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:131361000-131367600	Weak transcription	Brain Substantia Nigra	brain
16	chr6:131361400-131373800	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:131361600-131369000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:131362800-131366600	Weak transcription	Brain Anterior Caudate	brain
19	chr6:131363800-131371400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:131364000-131372200	Weak transcription	NHLF	lung
21	chr6:131364200-131370000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:131364400-131368600	Weak transcription	Ovary	ovary
23	chr6:131364400-131369600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:131364400-131370000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:131364400-131372600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:131364400-131374600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:131364600-131369600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:131364800-131366600	Weak transcription	HepG2	liver
29	chr6:131364800-131369600	Weak transcription	NHDF-Ad	bronchial

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