Variant report

Variant	rs2813702
Chromosome Location	chr1:216913500-216913501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1339352	0.83[YRI][hapmap]
rs2789734	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2813703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2813704	0.83[YRI][hapmap]
rs871556	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs871557	0.83[YRI][hapmap]
rs946473	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs946474	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs946475	1.00[CEU][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs946476	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs956543	0.81[JPT][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	nsv508694	chr1:216901014-216923883	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2813702	LPGAT1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216897400-216958600	Weak transcription	Pancreas	Pancrea
2	chr1:216911600-216934200	Weak transcription	Psoas Muscle	Psoas
3	chr1:216912200-216914400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:216912600-216914000	Enhancers	Fetal Heart	heart
5	chr1:216912800-216913800	Enhancers	H9 Cell Line	embryonic stem cell
6	chr1:216912800-216914400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:216913000-216913800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:216913000-216913800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:216913000-216914000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:216913000-216914200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:216913000-216914400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:216913200-216914000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:216913200-216914200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:216913400-216913600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:216913400-216913600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr1:216913400-216913800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:216913400-216914000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:216913400-216914400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:216913400-216914600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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