Variant report

Variant	rs227843
Chromosome Location	chr6:44691703-44691704
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	chr6:44681103..44683539-chr6:44690355..44693257,2	MCF-7	breast:
2	chr6:44691206..44694141-chr6:44700242..44701897,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1022730	0.96[ASN][1000 genomes]
rs1022731	0.96[ASN][1000 genomes]
rs12215252	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1338907	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1342640	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1418433	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1832897	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2145826	0.81[ASN][1000 genomes]
rs227831	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs227837	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs227838	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs227841	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227847	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs227848	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227849	0.93[CEU][hapmap];0.95[TSI][hapmap]
rs227850	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs227851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs227854	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs227855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799968	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs6458412	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6910294	0.85[CEU][hapmap]
rs6933373	0.81[ASN][1000 genomes]
rs911524	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9349303	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.84[TSI][hapmap]
rs9369514	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs9369515	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9369516	0.80[TSI][hapmap]
rs9395051	0.80[TSI][hapmap]
rs9463011	0.82[ASN][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs227843	SUPT3H	cis	parietal	SCAN
rs227843	C6orf226	cis	cerebellum	SCAN
rs227843	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs227843	SUPT3H	cis	lymphoblastoid	seeQTL
rs227843	SUPT3H	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44689600-44693200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:44690200-44691800	Enhancers	Brain Germinal Matrix	brain
3	chr6:44690200-44693200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:44690400-44698000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:44691000-44691800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr6:44691000-44691800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:44691000-44692000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:44691000-44692000	Enhancers	Spleen	Spleen
9	chr6:44691200-44691800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:44691200-44691800	Enhancers	HSMMtube	muscle
11	chr6:44691400-44692600	Weak transcription	Adipose Nuclei	Adipose
12	chr6:44691400-44692800	Weak transcription	Right Atrium	heart
13	chr6:44691400-44695400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:44691600-44693000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:44691600-44695400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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