Variant report

Variant	rs6453644
Chromosome Location	chr6:73865196-73865197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	6:73859137-73881637..6:73927031-73938730	Hela-S3	cervix:
2	6:73859137-73881637..6:74062967-74076046	GM12878	blood:
3	6:73859137-73881637..6:74099986-74112890	GM12878	blood:

Variant related genes	Relation type
ENSG00000238464	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000256980	Chromatin interaction
ENSG00000224221	Chromatin interaction
ENSG00000203909	Chromatin interaction
ENSG00000203908	Chromatin interaction
ENSG00000203907	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1815728	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1815729	0.80[AMR][1000 genomes]
rs1970547	0.87[ASW][hapmap]
rs1974369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027544	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2350387	0.87[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs2350389	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35034898	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4235874	0.88[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6453645	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6453646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6453648	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6453649	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6907229	0.87[ASW][hapmap]
rs6939575	1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7747411	0.80[AMR][1000 genomes]
rs7748250	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7748418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7762949	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7763514	0.85[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs7769085	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs884957	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9343011	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs947747	0.80[AMR][1000 genomes]
rs947748	0.87[ASW][hapmap];0.84[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs952880	0.83[GIH][hapmap]

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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6453644	SGCA	trans	cerebellum	SCAN
rs6453644	XAGE5	trans	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73844400-73867000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:73844600-73865200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:73844800-73866400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:73846000-73866400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:73846400-73879200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:73854600-73867200	Weak transcription	Aorta	Aorta
7	chr6:73856200-73866400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:73856600-73876600	Weak transcription	Primary B cells from cord blood	blood
9	chr6:73863200-73876400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:73863600-73878000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:73865000-73867200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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