Variant report

Variant	rs11693376
Chromosome Location	chr2:73018806-73018807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10204141	0.92[ASN][1000 genomes]
rs1032982	0.82[CEU][hapmap]
rs11126381	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11126384	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11676555	0.82[CEU][hapmap]
rs11679683	0.82[CEU][hapmap]
rs11686536	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12476137	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12479094	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12615163	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12994646	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13006497	1.00[LWK][hapmap]
rs13008515	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]
rs1396107	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1508060	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1508061	0.82[CEU][hapmap]
rs1532970	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876489	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876490	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1911690	0.82[CEU][hapmap]
rs2068410	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2135982	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2420882	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35666345	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4597553	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4852889	0.82[CEU][hapmap]
rs4852890	0.82[CEU][hapmap]
rs4852891	0.86[CEU][hapmap]
rs4852896	0.82[ASN][1000 genomes]
rs6546781	0.82[CEU][hapmap]
rs6546787	0.83[EUR][1000 genomes]
rs6727086	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6744758	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6758539	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6758802	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7583914	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7586339	0.92[ASN][1000 genomes]
rs7586886	0.82[ASN][1000 genomes]
rs7588400	0.82[CEU][hapmap]
rs7600718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs970577	0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[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
rs11693376	TGFA	cis	cerebellum	SCAN
rs11693376	STAMBP	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72991200-73023000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:72999800-73022000	Weak transcription	Right Ventricle	heart
3	chr2:73008600-73020600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:73009200-73021000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:73010200-73021000	Weak transcription	Brain Anterior Caudate	brain
6	chr2:73010400-73020400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:73011800-73020800	Weak transcription	Fetal Lung	lung
8	chr2:73011800-73021200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:73013200-73020400	Weak transcription	Fetal Stomach	stomach
10	chr2:73014000-73020800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:73014000-73033400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:73015000-73021000	Weak transcription	Lung	lung
13	chr2:73016000-73019200	Enhancers	Fetal Heart	heart
14	chr2:73016400-73035600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:73016600-73020600	Weak transcription	HSMMtube	muscle
16	chr2:73016600-73020800	Weak transcription	Brain Angular Gyrus	brain
17	chr2:73016600-73020800	Weak transcription	NHDF-Ad	bronchial
18	chr2:73016600-73021000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:73016600-73021000	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:73016600-73021000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:73016600-73021000	Weak transcription	Brain Substantia Nigra	brain
22	chr2:73016600-73021000	Weak transcription	HUVEC	blood vessel
23	chr2:73016600-73021000	Weak transcription	Osteobl	bone
24	chr2:73016600-73021200	Weak transcription	NHLF	lung
25	chr2:73016600-73021400	Weak transcription	NH-A	brain
26	chr2:73016600-73022000	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:73016600-73035800	Weak transcription	Left Ventricle	heart
28	chr2:73016800-73020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:73016800-73020800	Weak transcription	HSMM	muscle
30	chr2:73016800-73021000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:73016800-73021200	Weak transcription	A549	lung
32	chr2:73016800-73021200	Weak transcription	Hela-S3	cervix
33	chr2:73016800-73021400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:73017200-73021200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:73017400-73021000	Weak transcription	HMEC	breast
36	chr2:73017600-73020800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:73018200-73021000	Weak transcription	NHEK	skin
38	chr2:73018200-73021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:73018800-73021600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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