Variant report

Variant	rs256980
Chromosome Location	chr5:114902807-114902808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114869947..114871868-chr5:114902039..114905014,2	K562	blood:
2	chr5:114893635..114896285-chr5:114902455..114905206,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12187973	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs171774	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs173965	0.87[ASN][1000 genomes]
rs173966	0.82[ASN][1000 genomes]
rs187682	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2546484	0.85[CEU][hapmap]
rs2546486	0.81[JPT][hapmap]
rs2546487	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2559990	0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs256938	0.85[CEU][hapmap]
rs256943	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[ASN][1000 genomes]
rs256944	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs256945	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs256956	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs256959	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs256962	0.85[GIH][hapmap]
rs256964	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs256967	0.85[ASN][1000 genomes]
rs256968	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs256970	0.86[ASN][1000 genomes]
rs256971	0.85[ASN][1000 genomes]
rs256972	0.85[ASN][1000 genomes]
rs256976	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256978	0.83[ASN][1000 genomes]
rs256984	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs256986	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256987	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs256988	0.84[ASN][1000 genomes]
rs256991	0.84[ASN][1000 genomes]
rs256993	0.84[ASN][1000 genomes]
rs256994	0.94[ASN][1000 genomes]
rs256996	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.94[ASN][1000 genomes]
rs256997	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs256998	0.82[ASN][1000 genomes]
rs372702	0.85[CEU][hapmap]
rs387718	0.93[ASN][1000 genomes]
rs415577	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs419939	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs424434	0.82[GIH][hapmap];0.82[MEX][hapmap]
rs6893854	0.82[CEU][hapmap]
rs6894123	0.82[CEU][hapmap]
rs813761	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9326969	0.80[GIH][hapmap];0.82[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
rs256980	DCP2	cis	parietal	SCAN
rs256980	SEMA6A	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114894000-114907200	Weak transcription	Pancreas	Pancrea
2	chr5:114894600-114907000	Weak transcription	Psoas Muscle	Psoas
3	chr5:114894600-114908800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:114895800-114907200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:114896200-114908400	Weak transcription	NH-A	brain
6	chr5:114901400-114906200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:114901400-114922400	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:114901600-114904400	Weak transcription	HSMMtube	muscle
9	chr5:114901600-114906400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:114902400-114911200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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