Variant report

Variant	rs6720889
Chromosome Location	chr2:72993493-72993494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10180259	0.96[EUR][1000 genomes]
rs11126378	0.85[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11689339	0.85[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap]
rs11892598	0.85[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs1562361	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs17008293	0.85[CEU][hapmap]
rs17008355	0.81[ASW][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]
rs17008360	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17008369	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17008371	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs55642420	0.95[EUR][1000 genomes]
rs56058174	0.95[EUR][1000 genomes]
rs59216875	0.94[EUR][1000 genomes]
rs60284189	0.95[EUR][1000 genomes]
rs61736520	0.96[EUR][1000 genomes]
rs66509842	0.96[EUR][1000 genomes]
rs66794803	0.95[EUR][1000 genomes]
rs6713143	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs6713712	0.85[CEU][hapmap]
rs6740390	0.84[CEU][hapmap]
rs67869181	0.80[EUR][1000 genomes]
rs67926386	0.95[EUR][1000 genomes]
rs72846963	0.88[EUR][1000 genomes]
rs7576726	0.81[ASW][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]
rs7604083	0.85[CEU][hapmap]

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	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6720889	TGFA	cis	cerebellum	SCAN
rs6720889	EXOC6B	cis	thalamus	BrainEAC
rs6720889	EXOC6B	cis	intralobular white matter	BrainEAC
rs6720889	MPHOSPH10	cis	cerebellum	SCAN
rs6720889	CD207	cis	cerebellum	SCAN
rs6720889	EXOC6B	cis	brain	BrainEAC

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72923000-73008600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:72981400-73000800	Weak transcription	Pancreas	Pancrea
3	chr2:72983200-72997800	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:72983200-72999200	Weak transcription	Left Ventricle	heart
5	chr2:72985200-72994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:72985200-73008400	Weak transcription	Right Atrium	heart
7	chr2:72985200-73015800	Weak transcription	Ovary	ovary
8	chr2:72989400-73015800	Weak transcription	Placenta	Placenta
9	chr2:72989600-73004000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:72990400-73006600	Weak transcription	Fetal Lung	lung
11	chr2:72990800-72995800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:72990800-72996000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:72990800-73018400	Weak transcription	Aorta	Aorta
14	chr2:72991200-72993800	Weak transcription	Fetal Brain Female	brain
15	chr2:72991200-72999800	Weak transcription	Fetal Intestine Small	intestine
16	chr2:72991200-73002200	Weak transcription	HepG2	liver
17	chr2:72991200-73015800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:72991200-73015800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:72991200-73023000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:72991400-72999400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:72992000-72999200	Weak transcription	Fetal Stomach	stomach
22	chr2:72992200-72995800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:72992200-73004600	Weak transcription	Lung	lung
24	chr2:72992400-72994400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:72992400-73007600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:72992600-72993600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:72992600-72993600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:72992600-72993800	Enhancers	Hela-S3	cervix
29	chr2:72992600-72993800	Enhancers	HMEC	breast
30	chr2:72992800-72993600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr2:72992800-72993600	Enhancers	HSMMtube	muscle
32	chr2:72992800-72993600	Flanking Active TSS	NHEK	skin
33	chr2:72993000-72993600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr2:72993000-72993600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr2:72993000-72993800	Enhancers	A549	lung
36	chr2:72993400-73002400	Weak transcription	Fetal Heart	heart

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