Variant report

Variant	rs2350387
Chromosome Location	chr6:73877424-73877425
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	chr6:73865237..73867807-chr6:73877060..73879197,2	K562	blood:
3	6:73859137-73881637..6:74062967-74076046	GM12878	blood:
4	6:73859137-73881637..6:74099986-74112890	GM12878	blood:

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

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1815726	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1815727	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1815728	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1815729	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1970547	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs1974369	0.87[ASW][hapmap];0.85[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes]
rs2027544	0.80[AMR][1000 genomes]
rs2882406	0.89[CEU][hapmap]
rs6453644	0.87[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs6453645	0.81[CEU][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6453646	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs6453649	0.85[YRI][hapmap]
rs6907229	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs6939575	0.87[GIH][hapmap]
rs7747411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7748418	0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7762949	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7763514	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7769085	0.88[CEU][hapmap]
rs884957	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9343011	0.87[GIH][hapmap];0.82[TSI][hapmap]
rs947747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs947748	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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
2	nsv1022151	chr6:73876795-73996828	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv538304	chr6:73876795-73996828	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2350387	KCNQ5	cis	cerebellum	SCAN
rs2350387	XAGE5	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73846400-73879200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:73863600-73878000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:73867000-73884600	Weak transcription	Primary T cells from cord blood	blood
4	chr6:73867400-73880600	Weak transcription	Aorta	Aorta
5	chr6:73867600-73890400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:73867600-73890400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:73869000-73904200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:73876400-73877800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:73876600-73878000	Strong transcription	Primary B cells from cord blood	blood
10	chr6:73876800-73878000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:73876800-73879200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:73876800-73889800	Weak transcription	HSMM	muscle
13	chr6:73877200-73877600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:73877200-73877800	Weak transcription	Psoas Muscle	Psoas
15	chr6:73877200-73878800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:73877200-73884200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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