Variant report

Variant	rs9430019
Chromosome Location	chr1:210050794-210050795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11579771	0.84[CHB][hapmap];0.93[CHD][hapmap];0.89[MEX][hapmap];0.89[YRI][hapmap];0.80[ASN][1000 genomes]
rs2049997	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2357231	0.82[LWK][hapmap];0.89[YRI][hapmap]
rs35967153	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4844497	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4844907	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583814	0.85[YRI][hapmap]
rs599663	0.81[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs615276	0.85[YRI][hapmap]
rs661755	0.85[YRI][hapmap]
rs684083	0.81[LWK][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.89[YRI][hapmap]
rs7548533	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9430019	LPGAT1	cis	cerebellum	SCAN
rs9430019	IRF6	cis	cerebellum	SCAN
rs9430019	SYT14	cis	Nerve Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210041000-210055400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:210045200-210051400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:210047400-210051200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:210047400-210051200	Enhancers	HMEC	breast
5	chr1:210047400-210052600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:210047400-210053400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:210048800-210050800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:210048800-210050800	Enhancers	HSMMtube	muscle
9	chr1:210048800-210051800	Enhancers	Hela-S3	cervix
10	chr1:210049000-210051200	Enhancers	NHDF-Ad	bronchial
11	chr1:210049200-210051000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:210049200-210051000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:210049200-210051000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:210049400-210051000	Enhancers	Brain Hippocampus Middle	brain
15	chr1:210049400-210052400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:210049400-210052400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:210049400-210052800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:210049400-210052800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:210049400-210056600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:210049800-210052200	Weak transcription	Brain Anterior Caudate	brain
21	chr1:210049800-210052200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:210049800-210052200	Weak transcription	Brain Substantia Nigra	brain
23	chr1:210049800-210052600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:210049800-210052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:210050000-210051200	Enhancers	NHEK	skin
26	chr1:210050000-210052400	Weak transcription	Brain Angular Gyrus	brain
27	chr1:210050000-210052800	Weak transcription	Osteobl	bone
28	chr1:210050200-210051200	Enhancers	HUVEC	blood vessel
29	chr1:210050200-210052400	Weak transcription	NH-A	brain
30	chr1:210050200-210052600	Weak transcription	HSMM	muscle
31	chr1:210050200-210052800	Weak transcription	Fetal Brain Female	brain
32	chr1:210050400-210052800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:210050600-210052200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:210050600-210052400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:210050600-210052600	Weak transcription	Brain Germinal Matrix	brain

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