Variant report

Variant	rs13008515
Chromosome Location	chr2:72986104-72986105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10204141	0.87[ASN][1000 genomes]
rs1032982	0.82[CEU][hapmap]
rs11126381	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11126384	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11676555	0.82[CEU][hapmap]
rs11679683	0.82[CEU][hapmap]
rs11686536	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11693376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12476137	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12479094	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12615163	1.00[JPT][hapmap]
rs12994646	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1396107	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1508060	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1508061	0.82[CEU][hapmap];0.80[AFR][1000 genomes]
rs1532970	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1876489	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1876490	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1911690	0.82[CEU][hapmap]
rs2068410	0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs2135982	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2420882	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35666345	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4597553	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4852889	0.82[CEU][hapmap]
rs4852890	0.82[CEU][hapmap]
rs4852891	0.86[CEU][hapmap]
rs6546781	0.82[CEU][hapmap]
rs6546787	0.83[EUR][1000 genomes]
rs6727086	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6744758	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6758539	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6758802	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7583914	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7586339	0.87[ASN][1000 genomes]
rs7588400	0.82[CEU][hapmap]
rs7600718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970577	0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13008515	TGFA	cis	cerebellum	SCAN
rs13008515	STAMBP	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr2:72938200-72987800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:72976000-72988400	Weak transcription	Fetal Lung	lung
4	chr2:72981400-73000800	Weak transcription	Pancreas	Pancrea
5	chr2:72982200-72987600	Enhancers	Fetal Heart	heart
6	chr2:72982800-72988800	Weak transcription	Fetal Stomach	stomach
7	chr2:72983000-72989000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:72983200-72988600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:72983200-72997800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:72983200-72999200	Weak transcription	Left Ventricle	heart
11	chr2:72983400-72986200	Weak transcription	Brain Substantia Nigra	brain
12	chr2:72983400-72986600	Weak transcription	Right Ventricle	heart
13	chr2:72983800-72990200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:72984000-72990400	Weak transcription	NH-A	brain
15	chr2:72984200-72992800	Weak transcription	HSMM	muscle
16	chr2:72984600-72986800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:72984800-72993200	Weak transcription	Osteobl	bone
18	chr2:72985000-72988000	Weak transcription	Fetal Intestine Small	intestine
19	chr2:72985200-72986400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:72985200-72987600	Enhancers	HepG2	liver
21	chr2:72985200-72988000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:72985200-72990000	Weak transcription	NHEK	skin
23	chr2:72985200-72990200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:72985200-72990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:72985200-72994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:72985200-73008400	Weak transcription	Right Atrium	heart
27	chr2:72985200-73015800	Weak transcription	Ovary	ovary
28	chr2:72985600-72987600	Weak transcription	A549	lung
29	chr2:72986000-72986400	Enhancers	Stomach Mucosa	stomach
30	chr2:72986000-72987000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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