Variant report

Variant	rs828847
Chromosome Location	chr2:74353440-74353441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74346232..74350107-chr2:74352488..74356808,10	K562	blood:
2	chr2:74347502..74349512-chr2:74350622..74354565,3	K562	blood:
3	chr2:74326343..74328844-chr2:74352521..74354991,2	MCF-7	breast:
4	chr2:74351961..74355354-chr2:74404780..74407747,5	K562	blood:
5	chr2:74351961..74355354-chr2:74404780..74407747,4	K562	blood:

Variant related genes	Relation type
ENSG00000257800	Chromatin interaction
ENSG00000114978	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1026150	1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1095969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1095970	0.95[ASN][1000 genomes]
rs12465641	0.86[JPT][hapmap]
rs12996870	0.94[ASN][1000 genomes]
rs13025827	0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs1667615	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1667616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1667622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1723283	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1723284	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1723290	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2122290	0.86[JPT][hapmap]
rs2280642	0.85[JPT][hapmap]
rs2421753	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3099822	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3099823	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108161	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108162	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34284832	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35955502	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4429500	0.82[JPT][hapmap]
rs4452177	0.84[JPT][hapmap]
rs6707619	0.82[JPT][hapmap]
rs6758220	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs702463	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs702464	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs828841	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs828843	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828844	0.93[ASW][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs828845	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828846	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828848	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828850	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828864	0.86[ASN][1000 genomes]
rs828865	0.86[ASN][1000 genomes]
rs828867	0.90[JPT][hapmap]
rs828897	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828898	0.93[ASN][1000 genomes]
rs828901	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874285	chr2:74283728-74355244	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs828847	TPRKB	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74348000-74357400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:74348200-74355000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:74348200-74360400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:74348200-74367600	Weak transcription	Brain Anterior Caudate	brain
5	chr2:74348600-74361800	Weak transcription	Hela-S3	cervix
6	chr2:74348800-74360400	Weak transcription	Primary T cells from cord blood	blood
7	chr2:74350800-74360400	Weak transcription	Brain Substantia Nigra	brain
8	chr2:74351000-74353800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:74351200-74358400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:74353400-74360400	Weak transcription	Dnd41	blood

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