Variant report

Variant	rs10519960
Chromosome Location	chr5:127139966-127139967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10519953	0.95[CEU][hapmap];0.87[TSI][hapmap]
rs11241942	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11950864	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11957799	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1228156	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12653785	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1399829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1421747	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1515640	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1560673	0.91[CEU][hapmap];0.85[TSI][hapmap]
rs1849938	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1897525	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248689	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[TSI][hapmap]
rs248692	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[TSI][hapmap]
rs248709	0.95[CEU][hapmap];0.95[CHB][hapmap]
rs248724	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[TSI][hapmap]
rs2569146	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2569148	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2673772	0.90[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57883466	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59513079	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7714847	0.95[CEU][hapmap];0.95[CHB][hapmap]
rs790827	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs812059	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10519960	SLC12A2	cis	cerebellum	SCAN
rs10519960	LYRM7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127135200-127143800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr5:127138200-127140000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:127138200-127140200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:127138200-127140400	Weak transcription	NHEK	skin
5	chr5:127138200-127140600	Weak transcription	HSMM	muscle
6	chr5:127138200-127140600	Weak transcription	HSMMtube	muscle
7	chr5:127138400-127140000	Weak transcription	NH-A	brain
8	chr5:127138400-127140400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:127138400-127141400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:127138400-127141800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:127138600-127140600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:127138600-127140600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:127138600-127140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:127138600-127146400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:127138800-127140600	Weak transcription	NHDF-Ad	bronchial
16	chr5:127138800-127140600	Weak transcription	NHLF	lung
17	chr5:127139000-127145600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:127139200-127151800	Weak transcription	Stomach Mucosa	stomach
19	chr5:127139800-127140400	Enhancers	Colon Smooth Muscle	Colon

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