Variant report

Variant	rs3798387
Chromosome Location	chr6:117718813-117718814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13194436	0.93[EUR][1000 genomes]
rs13203726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204089	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs13211635	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13212382	0.90[EUR][1000 genomes]
rs13216390	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13216400	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13216409	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1321811	1.00[ASW][hapmap]
rs17574269	1.00[ASW][hapmap]
rs2243375	0.91[EUR][1000 genomes]
rs2243377	0.93[EUR][1000 genomes]
rs2243380	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2273603	0.85[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes]
rs34131577	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34231660	0.91[EUR][1000 genomes]
rs34258179	0.90[EUR][1000 genomes]
rs34280338	0.89[EUR][1000 genomes]
rs3777974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798386	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3798391	0.85[CHB][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs3798392	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs71570847	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71570849	0.91[EUR][1000 genomes]
rs9372479	0.85[CHB][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs9374654	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9385007	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9387467	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9387468	0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9387469	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9387472	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9387473	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9398457	0.81[CEU][hapmap]
rs9398458	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9401004	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs9401005	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9489138	0.86[JPT][hapmap];0.85[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	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv526934	chr6:117718303-117719528	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3798387	ROS1	cis	parietal	SCAN
rs3798387	MARCKS	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117692600-117735800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:117716400-117719600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:117716600-117730600	Weak transcription	HSMM	muscle
4	chr6:117718200-117728200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:117718600-117719200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:117718800-117719200	Enhancers	Fetal Brain Female	brain
7	chr6:117718800-117719200	Enhancers	HepG2	liver

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