Variant report

Variant	rs256976
Chromosome Location	chr5:114890507-114890508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114702805..114704848-chr5:114889870..114892622,2	K562	blood:
2	chr5:114878750..114881020-chr5:114889468..114892055,2	MCF-7	breast:
3	chr5:114879154..114881611-chr5:114889489..114893270,4	MCF-7	breast:
4	chr5:114836980..114838497-chr5:114890257..114892296,2	K562	blood:
5	chr5:114878777..114881689-chr5:114888906..114892048,4	K562	blood:

Variant related genes	Relation type
ENSG00000145780	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12187973	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs171774	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs173965	0.82[ASN][1000 genomes]
rs187682	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2546484	0.82[CEU][hapmap]
rs2546486	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs2546487	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2559990	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[ASN][1000 genomes]
rs256938	0.81[CEU][hapmap]
rs256940	0.82[CHB][hapmap]
rs256943	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs256944	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs256945	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs256956	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs256959	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs256962	0.83[GIH][hapmap];0.83[MEX][hapmap]
rs256964	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs256967	0.81[ASN][1000 genomes]
rs256968	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs256970	0.84[ASN][1000 genomes]
rs256971	0.83[ASN][1000 genomes]
rs256972	0.83[ASN][1000 genomes]
rs256978	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs256980	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256984	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs256986	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs256987	0.82[EUR][1000 genomes]
rs256994	0.89[ASN][1000 genomes]
rs256996	0.85[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[ASN][1000 genomes]
rs256997	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs372702	0.82[CEU][hapmap]
rs387718	0.89[ASN][1000 genomes]
rs415577	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs419939	0.80[CHB][hapmap]
rs424434	0.85[GIH][hapmap];0.87[MEX][hapmap]
rs6893854	0.82[CEU][hapmap]
rs6894123	0.82[CEU][hapmap]
rs813761	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9326969	0.83[GIH][hapmap];0.87[MEX][hapmap]

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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv830455	chr5:114761542-114938284	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1032234	chr5:114785557-114911527	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1796164	chr5:114854685-114936768	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs256976	SEMA6A	cis	cerebellum	SCAN
rs256976	DCP2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114881000-114893200	Weak transcription	Right Ventricle	heart
2	chr5:114886600-114893000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr5:114886800-114892200	Weak transcription	Gastric	stomach
4	chr5:114887400-114893200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:114887600-114890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:114887600-114890800	Weak transcription	NHLF	lung
7	chr5:114887600-114892200	Weak transcription	Pancreas	Pancrea
8	chr5:114887600-114893000	Weak transcription	Stomach Mucosa	stomach
9	chr5:114887600-114893200	Weak transcription	Esophagus	oesophagus
10	chr5:114887600-114893800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:114887800-114893800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:114888000-114892800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:114888200-114892800	Weak transcription	Right Atrium	heart
14	chr5:114888600-114892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:114889000-114893600	Weak transcription	NHDF-Ad	bronchial
16	chr5:114889400-114892600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:114889400-114895600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:114890400-114891400	Enhancers	HUVEC	blood vessel

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