Variant report

Variant	rs17304872
Chromosome Location	chr8:125936177-125936178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:125738536..125741882-chr8:125934456..125936858,4	MCF-7	breast:
2	chr8:125935909..125938271-chr8:125963994..125966987,3	MCF-7	breast:
3	chr8:125900994..125902188-chr8:125936157..125937195,3	MCF-7	breast:
4	chr8:125927702..125929777-chr8:125936123..125937814,2	MCF-7	breast:
5	chr8:125867918..125869705-chr8:125935657..125937307,2	MCF-7	breast:
6	chr8:125864651..125867984-chr8:125934838..125937619,3	MCF-7	breast:
7	chr8:125868680..125870635-chr8:125934172..125936239,2	MCF-7	breast:
8	chr8:125568500..125569404-chr8:125936057..125937539,6	MCF-7	breast:
9	chr8:125737610..125739305-chr8:125935041..125936937,2	MCF-7	breast:
10	chr8:125739577..125740559-chr8:125936039..125937070,5	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1052291	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11775219	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777190	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11780865	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787203	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11993071	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.80[ASN][1000 genomes]
rs17305012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17396442	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2077670	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34739489	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56073554	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6989608	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6990611	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs6997550	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7009560	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7814843	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1030803	chr8:125868684-125969635	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1024405	chr8:125868684-125971035	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1020502	chr8:125868684-125972572	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17304872	NSMCE2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125932800-125936800	Weak transcription	Right Atrium	heart
2	chr8:125933800-125936600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr8:125934000-125936800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr8:125934000-125937000	Weak transcription	Placenta	Placenta
5	chr8:125934400-125936400	Weak transcription	Fetal Heart	heart
6	chr8:125934400-125936400	Weak transcription	Left Ventricle	heart
7	chr8:125934400-125936600	Weak transcription	HepG2	liver
8	chr8:125934400-125937600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr8:125934600-125936400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr8:125935200-125937400	Enhancers	HMEC	breast
11	chr8:125935200-125937400	Enhancers	NHEK	skin
12	chr8:125935400-125936600	Enhancers	K562	blood
13	chr8:125935400-125937400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr8:125935400-125937400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr8:125935400-125937600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr8:125935800-125936800	Enhancers	Esophagus	oesophagus
17	chr8:125936000-125936400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr8:125936000-125937000	Enhancers	NHDF-Ad	bronchial

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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