Variant report

Variant	rs1927695
Chromosome Location	chr6:25378113-25378114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11967836	0.83[CHD][hapmap]
rs55731467	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57992726	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58095699	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58924292	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60556647	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73730705	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9461146	0.93[CEU][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9461147	0.93[CEU][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9461148	0.93[CEU][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9461149	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9467478	0.93[CEU][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9467480	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9467481	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1927695	BTN3A2	cis	parietal	SCAN
rs1927695	PRSS16	cis	cerebellum	SCAN
rs1927695	HIST1H2AG	cis	cerebellum	SCAN
rs1927695	LRRC16A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25368000-25378400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:25370400-25378400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:25370800-25388800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:25371400-25378400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:25375800-25378400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:25375800-25381200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:25377200-25378800	Enhancers	Right Atrium	heart
8	chr6:25377200-25379000	Enhancers	Fetal Thymus	thymus
9	chr6:25377400-25378600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:25377400-25378800	Enhancers	Aorta	Aorta
11	chr6:25377400-25379200	Enhancers	Thymus	Thymus
12	chr6:25377400-25410600	Weak transcription	Gastric	stomach
13	chr6:25377600-25378800	Enhancers	GM12878-XiMat	blood
14	chr6:25377800-25378400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:25377800-25395600	Weak transcription	Pancreas	Pancrea
16	chr6:25378000-25378400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:25378000-25378800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr6:25378000-25378800	Enhancers	Lung	lung
19	chr6:25378000-25379800	Weak transcription	Primary T helper naive cells fromperipheralblood	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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