Variant report

Variant	rs4680367
Chromosome Location	chr3:157166123-157166124
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1027603	0.81[JPT][hapmap]
rs10936086	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10936087	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs12486427	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs12496879	0.81[JPT][hapmap]
rs12638732	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1456097	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1500920	0.81[JPT][hapmap]
rs1546261	0.81[JPT][hapmap]
rs1568609	0.81[JPT][hapmap]
rs1585080	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1840668	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs1840680	0.88[ASW][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2305619	0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs2316706	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2316708	0.88[AMR][1000 genomes]
rs2316709	0.88[AMR][1000 genomes]
rs2316710	0.88[AMR][1000 genomes]
rs3816527	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816528	0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs4640512	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4680360	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs4680364	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6441126	0.90[JPT][hapmap]
rs6441128	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs6441129	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6803043	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6803236	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6803628	0.90[JPT][hapmap]
rs7609926	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7615621	0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7616177	0.88[AMR][1000 genomes]
rs7617727	0.82[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs7626884	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631556	0.81[JPT][hapmap]
rs7634847	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639254	0.82[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs9857875	0.81[JPT][hapmap]
rs9868133	0.88[AMR][1000 genomes]
rs9871290	0.82[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs988587	0.81[JPT][hapmap]
rs988588	0.81[JPT][hapmap]
rs9990136	0.81[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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4680367	PTX3	cis	cerebellum	SCAN
rs4680367	VEPH1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157159000-157177400	Weak transcription	NH-A	brain
2	chr3:157160400-157195000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:157160600-157176800	Weak transcription	Pancreas	Pancrea
4	chr3:157161200-157186600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:157162000-157171000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:157162400-157177000	Weak transcription	HSMM	muscle
7	chr3:157163800-157177000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:157164600-157169800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:157164600-157169800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:157164600-157185400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:157164800-157169400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:157164800-157169400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:157164800-157176800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:157165000-157169800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:157165200-157177200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:157165400-157169400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:157165600-157169600	Weak transcription	HUVEC	blood vessel
18	chr3:157165800-157167000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:157165800-157169400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr3:157165800-157170600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:157165800-157171000	Weak transcription	NHDF-Ad	bronchial
22	chr3:157165800-157174400	Weak transcription	Osteobl	bone

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