Variant report

Variant	rs1793410
Chromosome Location	chr11:75167704-75167705
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	ESR1	chr11:75167630-75168221	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr11:75167540-75168350	ECC-1	luminal epithelium:	n/a	chr11:75167756-75167766 chr11:75168063-75168071
3	EP300	chr11:75167379-75168309	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:75166133..75168077-chr11:75168681..75171144,2	K562	blood:
2	chr11:75159277..75162323-chr11:75164313..75168722,5	K562	blood:
3	chr11:75166849..75168397-chr11:75246511..75248333,2	MCF-7	breast:
4	chr11:75159277..75161641-chr11:75165363..75168722,5	K562	blood:
5	chr11:75165572..75168258-chr11:75186548..75189376,2	K562	blood:

Variant related genes	Relation type
GDPD5	TF binding region
ENSG00000158555	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1004856	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11236441	0.91[EUR][1000 genomes]
rs1540210	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1557471	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs1631470	0.90[CEU][hapmap];0.97[EUR][1000 genomes]
rs1790147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1790152	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1793414	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs2853066	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs499613	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs504793	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs511190	0.81[CHD][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs514477	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs540269	0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs544719	0.92[EUR][1000 genomes]
rs548439	0.94[EUR][1000 genomes]
rs549034	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs550881	0.90[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs566818	0.81[CHD][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs571353	0.90[CEU][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs581007	0.89[CEU][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs589724	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs628972	0.90[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs667410	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs669601	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs682292	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041640	chr11:74945824-75174688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
2	nsv897920	chr11:75087520-75181249	Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv897923	chr11:75129007-75302855	Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1793410	MYO7A	cis	parietal	SCAN
rs1793410	UCP3	cis	cerebellum	SCAN
rs1793410	CHCHD8	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75144200-75186600	Weak transcription	Gastric	stomach
2	chr11:75144400-75179800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:75144600-75174000	Weak transcription	Liver	Liver
4	chr11:75145000-75167800	Strong transcription	Placenta	Placenta
5	chr11:75145200-75186200	Weak transcription	Primary T cells from cord blood	blood
6	chr11:75145200-75186400	Strong transcription	Fetal Intestine Small	intestine
7	chr11:75146400-75173000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:75147800-75186000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr11:75148200-75186000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:75150400-75172600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:75153400-75168000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:75153800-75176600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr11:75159000-75172800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:75160600-75173000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:75161600-75176600	Weak transcription	Right Ventricle	heart
16	chr11:75162200-75171800	Weak transcription	NHDF-Ad	bronchial
17	chr11:75162600-75172400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:75162800-75185000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr11:75163800-75186200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr11:75164000-75174000	Weak transcription	Lung	lung
21	chr11:75165200-75187000	Strong transcription	HepG2	liver
22	chr11:75165400-75175400	Strong transcription	Fetal Intestine Large	intestine
23	chr11:75165800-75178000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:75166000-75168200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:75166000-75168600	Weak transcription	Adipose Nuclei	Adipose
26	chr11:75166200-75167800	Strong transcription	Spleen	Spleen
27	chr11:75166200-75176800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:75166400-75168400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:75166400-75169400	Strong transcription	HSMMtube	muscle
30	chr11:75166400-75178200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:75166600-75173000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:75166600-75186800	Weak transcription	Pancreas	Pancrea
33	chr11:75166800-75168000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:75166800-75168200	Strong transcription	Fetal Stomach	stomach
35	chr11:75166800-75172200	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:75166800-75174400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr11:75167000-75168400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:75167000-75172000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:75167200-75168400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr11:75167200-75168800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr11:75167200-75169200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr11:75167200-75171400	Weak transcription	Fetal Brain Female	brain
43	chr11:75167400-75167800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr11:75167400-75180400	Weak transcription	Aorta	Aorta

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