Variant report

Variant	rs7803397
Chromosome Location	chr7:38905686-38905687
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38900726..38902861-chr7:38904557..38906481,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10239557	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10242978	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10259755	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10266891	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10272767	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11980882	0.82[JPT][hapmap]
rs1229011	0.89[EUR][1000 genomes]
rs12532461	0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs1473137	0.81[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs17768753	0.82[JPT][hapmap]
rs1859937	0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2108507	0.82[JPT][hapmap]
rs2190666	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2240350	0.81[CHB][hapmap];0.81[CHD][hapmap]
rs2240355	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs2240555	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2286081	0.85[CHB][hapmap]
rs2286095	0.89[CHB][hapmap]
rs2286097	0.85[CHB][hapmap]
rs2286099	0.85[CHB][hapmap]
rs2392609	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.86[EUR][1000 genomes]
rs28722581	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2893567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35995292	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3779126	0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[LWK][hapmap]
rs3801135	1.00[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes]
rs4430003	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4720308	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4723793	1.00[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs56098802	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6462862	0.86[CHB][hapmap];0.81[CHD][hapmap];0.82[LWK][hapmap]
rs6961672	0.86[CHB][hapmap];0.82[LWK][hapmap]
rs7780625	0.82[JPT][hapmap]
rs7785161	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs7788664	0.81[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9638944	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7803397	TBX20	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:38871400-38905800	Weak transcription	Aorta	Aorta
3	chr7:38871400-38920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:38871600-38906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr7:38873000-38907600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:38873200-38919200	Weak transcription	Pancreas	Pancrea
7	chr7:38876400-38906200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:38879800-38938000	Weak transcription	Right Ventricle	heart
9	chr7:38881200-38907600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:38881200-38919200	Weak transcription	Psoas Muscle	Psoas
11	chr7:38883400-38907600	Weak transcription	Esophagus	oesophagus
12	chr7:38886200-38947800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr7:38886400-38907400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:38886400-38907400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr7:38886400-38907600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:38886600-38907200	Weak transcription	Colon Smooth Muscle	Colon
17	chr7:38887200-38906600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:38887200-38907400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:38889200-38907200	Weak transcription	Ovary	ovary
20	chr7:38889400-38906800	Weak transcription	Fetal Stomach	stomach
21	chr7:38889400-38907200	Weak transcription	Lung	lung
22	chr7:38889400-38907400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:38889400-38909600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:38889400-38948200	Weak transcription	Gastric	stomach
25	chr7:38889600-38932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:38893800-38925600	Weak transcription	Thymus	Thymus
27	chr7:38895200-38907200	Weak transcription	Brain Anterior Caudate	brain
28	chr7:38896000-38907600	Weak transcription	Spleen	Spleen
29	chr7:38896600-38906200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr7:38897600-38907400	Weak transcription	Brain Angular Gyrus	brain
31	chr7:38897600-38909000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr7:38898000-38907600	Weak transcription	HSMM	muscle
33	chr7:38898200-38907200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:38898200-38909200	Weak transcription	NH-A	brain
35	chr7:38898400-38920000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr7:38898600-38906800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:38898600-38907200	Weak transcription	Fetal Brain Female	brain
38	chr7:38898600-38907400	Weak transcription	HSMMtube	muscle
39	chr7:38898600-38907400	Weak transcription	Osteobl	bone
40	chr7:38898600-38907600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:38898600-38907600	Weak transcription	NHDF-Ad	bronchial
42	chr7:38898600-38914200	Weak transcription	NHLF	lung
43	chr7:38898600-38928800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr7:38898800-38906000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr7:38898800-38912200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr7:38899200-38905800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr7:38899200-38906400	Weak transcription	Fetal Brain Male	brain
48	chr7:38899200-38924200	Weak transcription	Fetal Kidney	kidney
49	chr7:38899400-38907600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr7:38900800-38907200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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