Variant report

Variant	rs9375794
Chromosome Location	chr6:131323855-131323856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr6:131323088-131323964	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131322346..131323948-chr6:131367071..131369025,2	K562	blood:
2	chr6:131322621..131325440-chr6:131350090..131351837,2	K562	blood:

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10457561	0.82[CEU][hapmap]
rs10457563	0.82[CEU][hapmap]
rs10872375	0.94[ASN][1000 genomes]
rs11154611	0.86[ASN][1000 genomes]
rs11760051	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12195366	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12196734	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12197829	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12203760	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]
rs12214021	0.96[ASN][1000 genomes]
rs13214846	0.83[AFR][1000 genomes]
rs1569195	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17059954	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1976981	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2151068	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2178282	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28812545	0.98[ASN][1000 genomes]
rs4259270	0.98[ASN][1000 genomes]
rs4498389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62423583	0.85[ASN][1000 genomes]
rs6901548	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6902930	0.98[ASN][1000 genomes]
rs6903705	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6905151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6907809	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6916206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6921542	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926372	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7763960	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7767569	0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs7770892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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]
rs9321264	0.89[ASN][1000 genomes]
rs9372986	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9372987	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9372989	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs9375784	0.84[ASN][1000 genomes]
rs9375785	0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9375787	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9375788	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9375789	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9375790	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9375795	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs9375796	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9375797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9388873	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9388876	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs9398967	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9398969	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9398970	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398972	0.98[ASN][1000 genomes]
rs9398973	0.98[ASN][1000 genomes]
rs9402301	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9402306	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402310	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9402313	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9402314	0.96[ASN][1000 genomes]
rs9483210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9492790	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9492792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs951251	0.94[ASN][1000 genomes]
rs954919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];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
rs9375794	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131314800-131325000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:131315800-131325800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:131318800-131325800	Weak transcription	Fetal Thymus	thymus
4	chr6:131318800-131328000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:131318800-131329200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:131319000-131324200	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:131319000-131324800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:131319000-131325000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:131319000-131325600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:131319400-131324800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:131319600-131324800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:131320400-131324600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:131320400-131325200	Weak transcription	Right Ventricle	heart
14	chr6:131321000-131324000	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr6:131321000-131326600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:131321400-131324000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr6:131321400-131325600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:131321800-131324000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:131321800-131324200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr6:131321800-131324200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:131321800-131327200	Enhancers	Fetal Stomach	stomach
22	chr6:131322000-131325600	Weak transcription	Stomach Mucosa	stomach
23	chr6:131322400-131325800	Weak transcription	Placenta	Placenta
24	chr6:131322400-131327000	Enhancers	Brain Substantia Nigra	brain
25	chr6:131322600-131324200	Enhancers	HepG2	liver
26	chr6:131322600-131325000	Weak transcription	Lung	lung
27	chr6:131322600-131325200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:131322600-131326600	Enhancers	Brain Hippocampus Middle	brain
29	chr6:131322600-131326800	Enhancers	Brain Cingulate Gyrus	brain
30	chr6:131322600-131327000	Enhancers	Brain Anterior Caudate	brain
31	chr6:131322600-131327000	Enhancers	Fetal Lung	lung
32	chr6:131322600-131333200	Weak transcription	Pancreas	Pancrea
33	chr6:131322800-131324800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:131323000-131324000	Enhancers	HSMM	muscle
35	chr6:131323000-131325600	Enhancers	Adipose Nuclei	Adipose
36	chr6:131323200-131324000	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr6:131323200-131324000	Enhancers	Small Intestine	intestine
38	chr6:131323200-131324200	Enhancers	Fetal Kidney	kidney
39	chr6:131323200-131324400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr6:131323200-131325200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:131323200-131325400	Enhancers	Osteobl	bone
42	chr6:131323200-131326000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:131323400-131325600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:131323600-131324400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:131323600-131324600	Weak transcription	Fetal Muscle Leg	muscle
46	chr6:131323600-131324600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:131323600-131324800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:131323600-131324800	Weak transcription	Brain Angular Gyrus	brain
49	chr6:131323600-131325000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:131323600-131325000	Weak transcription	H9 Cell Line	embryonic stem cell

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