Variant report

Variant	rs1473137
Chromosome Location	chr7:38886044-38886045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:38884593..38886823-chr7:38890906..38893182,2	MCF-7	breast:
2	chr7:38873915..38876598-chr7:38884159..38886331,2	MCF-7	breast:
3	chr7:38885810..38887445-chr7:38893961..38896931,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10242978	0.81[ASN][1000 genomes]
rs10266891	0.80[ASN][1000 genomes]
rs10272767	0.81[ASN][1000 genomes]
rs12532461	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1859937	0.82[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs2074656	0.95[CHB][hapmap]
rs2190666	0.81[CHB][hapmap]
rs2240350	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs2240352	0.82[JPT][hapmap]
rs2240355	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs2240555	0.85[JPT][hapmap]
rs2286081	0.85[CHB][hapmap]
rs2286095	0.83[CHB][hapmap]
rs2286097	0.85[CHB][hapmap]
rs2286099	0.85[CHB][hapmap]
rs2392609	0.86[JPT][hapmap]
rs2893567	0.81[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3779126	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3801135	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3801139	0.82[JPT][hapmap]
rs3801140	0.82[JPT][hapmap]
rs4430003	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4723793	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs56098802	0.80[ASN][1000 genomes]
rs6462862	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs6961672	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs7785161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7788664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7803397	0.81[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs9638944	0.81[CHB][hapmap];0.90[JPT][hapmap]

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	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1473137	TBX20	cis	parietal	SCAN
rs1473137	DPY19L1	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:38859000-38895200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:38859800-38900800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr7:38860600-38900200	Weak transcription	Fetal Intestine Large	intestine
7	chr7:38863000-38888200	Weak transcription	Fetal Intestine Small	intestine
8	chr7:38866000-38886400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:38867400-38905200	Weak transcription	Left Ventricle	heart
10	chr7:38869600-38888400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr7:38870000-38888200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr7:38870000-38895600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr7:38870200-38895600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr7:38871400-38905800	Weak transcription	Aorta	Aorta
15	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:38871600-38906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr7:38873000-38907600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr7:38873200-38889200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
20	chr7:38875800-38897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:38876400-38906200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:38877000-38895600	Weak transcription	Spleen	Spleen
23	chr7:38877200-38888200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:38877200-38900800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:38877200-38901200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr7:38877400-38888400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr7:38877400-38896200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr7:38878400-38888200	Weak transcription	Fetal Stomach	stomach
29	chr7:38879800-38891800	Weak transcription	Right Atrium	heart
30	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
31	chr7:38880200-38897600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr7:38880600-38888200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:38880600-38888800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:38880600-38888800	Weak transcription	Lung	lung
35	chr7:38880600-38900600	Weak transcription	Adipose Nuclei	Adipose
36	chr7:38880800-38888400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:38880800-38905600	Weak transcription	Fetal Muscle Leg	muscle
38	chr7:38881200-38888800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:38881200-38888800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:38881200-38895000	Weak transcription	GM12878-XiMat	blood
41	chr7:38881200-38898000	Weak transcription	HSMMtube	muscle
42	chr7:38881200-38898000	Weak transcription	NHLF	lung
43	chr7:38881200-38900000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:38881200-38907600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr7:38881200-38919200	Weak transcription	Psoas Muscle	Psoas
46	chr7:38881400-38898000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:38882000-38890200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:38883400-38907600	Weak transcription	Esophagus	oesophagus
49	chr7:38884400-38886800	Enhancers	Brain Hippocampus Middle	brain
50	chr7:38884600-38886800	Enhancers	Brain Substantia Nigra	brain

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