Variant report

Variant	rs227847
Chromosome Location	chr6:44695493-44695494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44629008..44631084-chr6:44694856..44697069,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1022730	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1022731	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12215252	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1338907	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1342640	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1418433	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1832897	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2145826	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs227831	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs227837	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs227838	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs227841	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs227843	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs227848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227849	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs227850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227854	0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs227855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799968	0.81[CEU][hapmap]
rs57020561	0.81[AMR][1000 genomes]
rs6458412	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6910294	0.85[CEU][hapmap]
rs911524	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9349303	0.85[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9369514	0.82[CEU][hapmap]
rs9369515	0.91[CHB][hapmap];0.84[AMR][1000 genomes]
rs9463011	0.81[AMR][1000 genomes]
rs9472339	0.90[EUR][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	esv1817071	chr6:44670110-44698829	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs227847	SUPT3H	cis	multi-tissue	Pritchard
rs227847	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44690400-44698000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:44693000-44698200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:44693200-44698400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:44694600-44698200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:44695400-44695600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:44695400-44695600	Flanking Active TSS	Placenta	Placenta
7	chr6:44695400-44695800	ZNF genes & repeats	Pancreas	Pancrea
8	chr6:44695400-44696000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:44695400-44696200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:44695400-44696400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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