Variant report

Variant	rs1540210
Chromosome Location	chr11:75209398-75209399
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75199608..75202442-chr11:75207814..75209873,2	K562	blood:
2	chr11:75186128..75188167-chr11:75208590..75210780,2	MCF-7	breast:
3	chr11:75209084..75211834-chr11:75212223..75216689,4	K562	blood:
4	chr11:75207844..75209994-chr11:75218744..75220757,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254460	Chromatin interaction
ENSG00000158555	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1004856	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs11236441	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1557471	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs1631470	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1783559	1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1790144	1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs1790147	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1790152	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793397	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1793410	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]
rs1793414	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs2853066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499613	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511190	0.82[EUR][1000 genomes]
rs514477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540269	0.81[EUR][1000 genomes]
rs544719	0.86[EUR][1000 genomes]
rs548439	0.87[EUR][1000 genomes]
rs549034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566818	0.82[EUR][1000 genomes]
rs571353	0.81[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs581007	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs589724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628972	1.00[CEU][hapmap];0.85[CHD][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs667410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669601	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs682292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[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	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
2	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1540210	MYO7A	cis	parietal	SCAN
rs1540210	ARAP1	cis	cerebellum	SCAN
rs1540210	KCTD21	cis	cerebellum	SCAN
rs1540210	FLJ33790	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75199400-75209800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:75200000-75219600	Weak transcription	Fetal Brain Female	brain
3	chr11:75202400-75210000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:75203800-75209800	Weak transcription	K562	blood
5	chr11:75203800-75210800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr11:75203800-75210800	Weak transcription	Colonic Mucosa	Colon
7	chr11:75203800-75217800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:75203800-75219200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr11:75204000-75216600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr11:75204200-75213400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:75204400-75210600	Weak transcription	Spleen	Spleen
12	chr11:75205600-75209800	Weak transcription	Right Ventricle	heart
13	chr11:75206600-75209800	Enhancers	A549	lung
14	chr11:75206800-75214200	Enhancers	Placenta	Placenta
15	chr11:75207000-75210800	Weak transcription	Gastric	stomach
16	chr11:75207200-75209800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr11:75207400-75209800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr11:75207400-75210200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr11:75207400-75216400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:75207600-75209400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:75207600-75209800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:75207600-75209800	Weak transcription	Psoas Muscle	Psoas
23	chr11:75207600-75210000	Weak transcription	Right Atrium	heart
24	chr11:75207600-75210600	Weak transcription	Lung	lung
25	chr11:75207600-75216400	Weak transcription	Left Ventricle	heart
26	chr11:75207800-75209400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:75207800-75209600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:75207800-75209600	Weak transcription	Fetal Intestine Large	intestine
29	chr11:75207800-75209600	Strong transcription	Fetal Intestine Small	intestine
30	chr11:75207800-75209800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:75207800-75210000	Weak transcription	Pancreas	Pancrea
32	chr11:75207800-75210200	Weak transcription	HUVEC	blood vessel
33	chr11:75207800-75210400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:75208200-75212200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:75208400-75209400	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:75208400-75209600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr11:75208400-75212400	Enhancers	HSMMtube	muscle
38	chr11:75208800-75209800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:75208800-75210200	Enhancers	Osteobl	bone
40	chr11:75208800-75210800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:75208800-75210800	Enhancers	HSMM	muscle
42	chr11:75208800-75211200	Genic enhancers	HepG2	liver
43	chr11:75209000-75210000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:75209000-75210200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:75209000-75212200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:75209000-75213400	Enhancers	Adipose Nuclei	Adipose
47	chr11:75209200-75211200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr11:75209200-75211400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr11:75209200-75211400	Enhancers	Colon Smooth Muscle	Colon
50	chr11:75209200-75211600	Flanking Active TSS	Hela-S3	cervix

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