Variant report

Variant	rs9388876
Chromosome Location	chr6:131345397-131345398
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	chr6:131345332..131348195-chr6:131348850..131352317,3	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10872375	0.93[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	0.93[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195366	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12196734	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][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[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203760	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12214021	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1569195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17059954	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1976981	0.98[ASN][1000 genomes]
rs2151068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178282	0.99[ASN][1000 genomes]
rs28812545	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259270	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]
rs4498389	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs62423583	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6901548	0.97[ASN][1000 genomes]
rs6902930	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903705	0.99[ASN][1000 genomes]
rs6905151	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs6907809	0.87[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6916206	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs6921542	0.99[ASN][1000 genomes]
rs6926372	0.97[ASN][1000 genomes]
rs7763960	0.98[ASN][1000 genomes]
rs7770892	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9321264	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9372986	0.91[ASN][1000 genomes]
rs9372987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs9372989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[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	0.86[CHB][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375787	0.93[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9375788	0.93[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9375789	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9375794	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs9375795	0.90[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9375796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375797	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9388873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9388880	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9398967	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398969	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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]
rs9398970	0.99[ASN][1000 genomes]
rs9398971	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9398972	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398973	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398975	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9398976	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9402301	0.85[ASN][1000 genomes]
rs9402306	0.91[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs9402310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9402313	0.99[ASN][1000 genomes]
rs9402314	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9483210	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9492790	0.95[ASN][1000 genomes]
rs9492792	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs951251	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs954919	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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
rs9388876	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 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	chr6:131337400-131347200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:131337800-131345400	Weak transcription	Right Atrium	heart
5	chr6:131337800-131351000	Weak transcription	Stomach Mucosa	stomach
6	chr6:131339400-131349400	Weak transcription	Brain Angular Gyrus	brain
7	chr6:131343600-131345400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:131344200-131345400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:131344400-131347600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:131345000-131345400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:131345000-131345400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:131345000-131345600	Flanking Active TSS	HMEC	breast
13	chr6:131345000-131345600	Flanking Active TSS	NHDF-Ad	bronchial
14	chr6:131345000-131345800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:131345000-131345800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:131345000-131345800	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr6:131345000-131345800	Enhancers	HSMM	muscle
18	chr6:131345000-131345800	Enhancers	HSMMtube	muscle
19	chr6:131345000-131345800	Flanking Active TSS	NHEK	skin
20	chr6:131345000-131346000	Enhancers	A549	lung
21	chr6:131345000-131346000	Enhancers	HUVEC	blood vessel
22	chr6:131345000-131346000	Enhancers	Osteobl	bone
23	chr6:131345000-131347000	Enhancers	NHLF	lung
24	chr6:131345000-131348000	Enhancers	Brain Anterior Caudate	brain
25	chr6:131345000-131348800	Enhancers	Brain Hippocampus Middle	brain
26	chr6:131345200-131345400	Flanking Active TSS	Hela-S3	cervix
27	chr6:131345200-131345600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:131345200-131345600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:131345200-131345600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:131345200-131345600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:131345200-131345600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr6:131345200-131345600	Enhancers	Adipose Nuclei	Adipose
33	chr6:131345200-131345600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr6:131345200-131345800	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr6:131345200-131345800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:131345200-131345800	Enhancers	Brain Cingulate Gyrus	brain
37	chr6:131345200-131345800	Enhancers	Fetal Muscle Leg	muscle
38	chr6:131345200-131345800	Enhancers	Ovary	ovary
39	chr6:131345200-131345800	Enhancers	Small Intestine	intestine
40	chr6:131345200-131346000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:131345200-131346000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:131345200-131346000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:131345200-131346000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:131345200-131346000	Enhancers	Colon Smooth Muscle	Colon
45	chr6:131345200-131346000	Enhancers	HepG2	liver
46	chr6:131345200-131346000	Enhancers	NH-A	brain
47	chr6:131345200-131346200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:131345200-131348000	Enhancers	Brain Substantia Nigra	brain

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