Variant report

Variant	rs12203760
Chromosome Location	chr6:131349617-131349618
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: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10457561	0.82[CEU][hapmap]
rs10457563	0.82[CEU][hapmap]
rs10457565	0.82[AFR][1000 genomes]
rs10872375	0.96[ASN][1000 genomes]
rs11154611	0.86[ASN][1000 genomes]
rs11760051	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12195366	0.82[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12196734	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs12197829	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12214021	0.98[ASN][1000 genomes]
rs1569195	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17059954	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1976981	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2151068	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2178282	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28812545	0.99[ASN][1000 genomes]
rs4259270	0.99[ASN][1000 genomes]
rs4498389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62423583	0.85[ASN][1000 genomes]
rs6901548	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902930	0.99[ASN][1000 genomes]
rs6903705	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6907809	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6916206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6921207	0.83[GIH][hapmap]
rs6921542	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926372	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6935560	0.94[LWK][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs7763960	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7770892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs9321264	0.88[ASN][1000 genomes]
rs9372986	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9372987	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9372989	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9375784	0.84[ASN][1000 genomes]
rs9375785	0.87[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9375787	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9375788	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9375789	0.91[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9375790	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9375794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9375795	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9375796	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9375797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388873	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9388876	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9398967	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9398969	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9398970	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398971	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398972	0.99[ASN][1000 genomes]
rs9398973	0.99[ASN][1000 genomes]
rs9402301	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9402306	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9402310	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9402313	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402314	0.98[ASN][1000 genomes]
rs9483210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9492790	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9492792	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951251	0.96[ASN][1000 genomes]
rs954919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs12203760	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131337800-131351000	Weak transcription	Stomach Mucosa	stomach
2	chr6:131345600-131350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:131345600-131350600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:131345600-131350800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:131345600-131351000	Weak transcription	Right Ventricle	heart
6	chr6:131345800-131350000	Weak transcription	HSMMtube	muscle
7	chr6:131345800-131350200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:131345800-131350200	Weak transcription	HSMM	muscle
9	chr6:131345800-131350600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:131345800-131350600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:131345800-131350600	Weak transcription	NHEK	skin
12	chr6:131345800-131350800	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:131345800-131351000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:131345800-131351000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:131345800-131351200	Weak transcription	Right Atrium	heart
16	chr6:131345800-131352000	Weak transcription	Lung	lung
17	chr6:131345800-131353200	Weak transcription	Ovary	ovary
18	chr6:131345800-131353800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:131345800-131357600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:131346000-131350000	Weak transcription	A549	lung
21	chr6:131346000-131350000	Weak transcription	HepG2	liver
22	chr6:131346000-131350200	Weak transcription	NH-A	brain
23	chr6:131346000-131350400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:131346000-131351200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:131346000-131351200	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:131346000-131375000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:131346200-131350000	Weak transcription	GM12878-XiMat	blood
28	chr6:131346200-131351200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:131347000-131350800	Weak transcription	NHLF	lung
30	chr6:131347600-131350000	Weak transcription	NHDF-Ad	bronchial
31	chr6:131347600-131350600	Weak transcription	Osteobl	bone
32	chr6:131347600-131351200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:131347800-131350800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:131347800-131350800	Weak transcription	Fetal Kidney	kidney
35	chr6:131348000-131350000	Weak transcription	Brain Anterior Caudate	brain
36	chr6:131348000-131350000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:131348000-131350200	Weak transcription	Brain Substantia Nigra	brain
38	chr6:131348000-131350800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:131348000-131350800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:131348000-131351000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:131348000-131351000	Weak transcription	Small Intestine	intestine
42	chr6:131348000-131351200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:131348000-131351200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:131348200-131350000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:131348600-131351600	Enhancers	Adipose Nuclei	Adipose
46	chr6:131348800-131350000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:131348800-131350200	Weak transcription	Brain Hippocampus Middle	brain
48	chr6:131348800-131351000	Weak transcription	Psoas Muscle	Psoas
49	chr6:131348800-131351200	Weak transcription	Left Ventricle	heart
50	chr6:131348800-131351400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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