Variant report

Variant	rs2980869
Chromosome Location	chr8:126488250-126488251
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:126487251..126488761-chr8:126508249..126510856,2	MCF-7	breast:
2	chr8:126441723..126444081-chr8:126487390..126489417,3	MCF-7	breast:
3	chr8:126487669..126490463-chr8:126500662..126505453,4	MCF-7	breast:
4	chr8:126439120..126443279-chr8:126483208..126489107,6	MCF-7	breast:
5	chr8:126487201..126489383-chr8:126491210..126493652,2	K562	blood:
6	chr8:126487883..126490527-chr8:126491210..126493645,2	K562	blood:
7	chr8:126488058..126489576-chr8:126500538..126503490,2	MCF-7	breast:
8	chr8:126481379..126484101-chr8:126487149..126489863,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000173334	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10808546	0.85[EUR][1000 genomes]
rs17321515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2001846	0.89[ASN][1000 genomes]
rs2001945	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs2954017	0.85[ASN][1000 genomes]
rs2954019	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2954021	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2954022	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2954025	0.84[ASW][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2954029	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2954030	0.90[YRI][hapmap]
rs2954031	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2980853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2980854	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2980855	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2980856	1.00[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs2980860	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2980871	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2980875	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980882	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2980886	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6982502	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6982636	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6999569	0.94[EUR][1000 genomes]
rs7828113	1.00[YRI][hapmap];0.88[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891437	chr8:126470817-126629328	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2980869	HAS2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:126479400-126489200	Weak transcription	Pancreas	Pancrea
2	chr8:126483000-126489400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:126483000-126498200	Weak transcription	Right Atrium	heart
4	chr8:126483200-126489000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr8:126483200-126489400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr8:126483400-126496600	Weak transcription	Hela-S3	cervix
7	chr8:126487000-126490000	Enhancers	Placenta	Placenta
8	chr8:126487200-126492400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:126487400-126489600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:126487600-126491800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr8:126487600-126492000	Weak transcription	NHEK	skin
12	chr8:126487600-126493200	Weak transcription	HMEC	breast
13	chr8:126487600-126496600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr8:126488000-126489000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr8:126488000-126489200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr8:126488000-126497200	Weak transcription	Liver	Liver

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