Variant report

Variant	rs11770381
Chromosome Location	chr7:138301034-138301035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11974460	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12707390	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1628052	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1659815	0.82[YRI][hapmap]
rs1659821	0.96[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1673221	0.85[EUR][1000 genomes]
rs1673222	0.81[EUR][1000 genomes]
rs1673224	0.86[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1673225	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11770381	SLC13A4	cis	parietal	SCAN
rs11770381	ZC3HAV1L	cis	cerebellum	SCAN
rs11770381	BRAF	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138287600-138303200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:138293200-138308400	Weak transcription	Primary T cells from cord blood	blood
3	chr7:138296400-138303600	Weak transcription	Fetal Intestine Small	intestine
4	chr7:138297400-138307400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:138297600-138318800	Weak transcription	Hela-S3	cervix
6	chr7:138298800-138303200	Weak transcription	Pancreas	Pancrea
7	chr7:138299000-138303400	Weak transcription	Liver	Liver
8	chr7:138299200-138303600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:138299800-138302200	Weak transcription	Fetal Kidney	kidney
10	chr7:138300000-138302400	Weak transcription	HepG2	liver
11	chr7:138300800-138301200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr7:138301000-138301200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr7:138301000-138302600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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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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