Variant report

Variant	rs11590711
Chromosome Location	chr1:165813862-165813863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165812134..165815476-chr1:165816977..165818639,3	K562	blood:
2	chr1:165654373..165656083-chr1:165811609..165814179,2	K562	blood:
3	chr1:165798053..165799867-chr1:165811993..165814835,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10737519	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753694	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800162	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10918291	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10918294	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12041574	0.82[CHB][hapmap]
rs1934275	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2185268	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34800847	0.92[ASN][1000 genomes]
rs4483381	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4535982	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4548416	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs4657481	0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426941	0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs6677965	0.95[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[ASN][1000 genomes]
rs6678380	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs6682894	0.94[ASN][1000 genomes]
rs6684773	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.97[ASN][1000 genomes]
rs6686237	0.89[ASN][1000 genomes]
rs6690966	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6702462	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7517175	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539793	0.87[ASN][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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv2830094	chr1:165785503-165840411	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
3	nsv548097	chr1:165797966-165825166	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
4	esv2755529	chr1:165813862-165858354	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11590711	TOMM40L	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165798800-165814200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:165799000-165818200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:165799200-165815800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:165808200-165814200	Enhancers	Duodenum Mucosa	Duodenum
5	chr1:165810800-165814000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr1:165810800-165814000	Enhancers	Small Intestine	intestine
7	chr1:165810800-165814400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:165810800-165817000	Enhancers	Fetal Thymus	thymus
9	chr1:165811000-165814000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:165811200-165817000	Enhancers	Thymus	Thymus
11	chr1:165812000-165814200	Weak transcription	Fetal Brain Female	brain
12	chr1:165812000-165816600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:165812200-165820200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:165812200-165820200	Weak transcription	Spleen	Spleen
15	chr1:165812200-165823200	Weak transcription	Aorta	Aorta
16	chr1:165812200-165823200	Weak transcription	Fetal Stomach	stomach
17	chr1:165812200-165823400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:165812400-165814400	Enhancers	Dnd41	blood
19	chr1:165812400-165815000	Weak transcription	HepG2	liver
20	chr1:165812400-165815600	Enhancers	K562	blood
21	chr1:165812400-165818400	Weak transcription	Right Atrium	heart
22	chr1:165812400-165820200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:165812400-165820200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:165812400-165820200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:165812400-165820200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:165812400-165820200	Weak transcription	HSMMtube	muscle
27	chr1:165812400-165820400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:165812400-165820400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:165812400-165821800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:165812400-165822200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:165812400-165823200	Weak transcription	Left Ventricle	heart
32	chr1:165812400-165823200	Weak transcription	Right Ventricle	heart
33	chr1:165812400-165823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:165812600-165814400	Enhancers	A549	lung
35	chr1:165812600-165820200	Weak transcription	Fetal Intestine Small	intestine
36	chr1:165812600-165820400	Weak transcription	Fetal Heart	heart
37	chr1:165812600-165821800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr1:165812800-165814800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:165812800-165815600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:165812800-165818400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:165812800-165818400	Weak transcription	HMEC	breast
42	chr1:165812800-165820200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:165812800-165820200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:165812800-165820200	Weak transcription	NHEK	skin
45	chr1:165812800-165820200	Weak transcription	Osteobl	bone
46	chr1:165813000-165814200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:165813000-165814800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:165813000-165814800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:165813000-165815000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:165813000-165815000	Weak transcription	Lung	lung

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