Variant report

Variant	rs2744572
Chromosome Location	chr6:24490511-24490512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:24490219-24490512	MCF-7	breast:	n/a	chr6:24490286-24490297 chr6:24490285-24490302
2	FOS	chr6:24490119-24490513	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24490344..24492283-chr6:24493726..24496491,4	MCF-7	breast:
2	chr6:24487096..24491354-chr6:24491448..24495730,8	K562	blood:
3	chr6:24488265..24492557-chr6:24493494..24498787,7	K562	blood:
4	chr6:24489101..24491684-chr6:24493403..24495493,2	MCF-7	breast:

Variant related genes	Relation type
GPLD1	TF binding region
ALDH5A1	TF binding region
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1569579	0.82[CHB][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs2010190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744551	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2744554	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2744555	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2744582	0.90[ASN][1000 genomes]
rs2744588	0.87[ASN][1000 genomes]
rs2744594	0.85[MEX][hapmap]
rs2744597	0.85[MEX][hapmap]
rs2760137	0.87[ASN][1000 genomes]
rs2760138	0.83[CHB][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs2760146	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2760153	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793444	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2793445	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817204	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2817215	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817217	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2817218	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2817226	0.87[ASN][1000 genomes]
rs2817227	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2817231	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2817247	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2817248	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs807519	0.85[MEX][hapmap]
rs807527	0.80[MEX][hapmap]
rs807531	0.80[MEX][hapmap]
rs941437	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763542	chr6:24445131-24520637	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv519552	chr6:24451256-24524704	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv883480	chr6:24481299-24507519	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24429000-24494200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:24458800-24492800	Weak transcription	Thymus	Thymus
3	chr6:24458800-24494000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:24470600-24494600	Weak transcription	Left Ventricle	heart
5	chr6:24473000-24494600	Weak transcription	Ovary	ovary
6	chr6:24480400-24493600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:24483800-24494000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:24485400-24494000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:24488000-24492000	Enhancers	Fetal Muscle Leg	muscle
10	chr6:24489000-24490600	Enhancers	Adipose Nuclei	Adipose
11	chr6:24489000-24491600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr6:24489400-24490600	Enhancers	HepG2	liver
13	chr6:24489600-24492000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr6:24489800-24494600	Weak transcription	Right Atrium	heart
15	chr6:24490200-24490600	Enhancers	Colon Smooth Muscle	Colon
16	chr6:24490200-24490600	Enhancers	Hela-S3	cervix
17	chr6:24490200-24490800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:24490400-24490800	Enhancers	Brain Anterior Caudate	brain
19	chr6:24490400-24492000	Enhancers	Fetal Muscle Trunk	muscle
20	chr6:24490400-24492200	Enhancers	Liver	Liver
21	chr6:24490400-24494400	Weak transcription	Right Ventricle	heart
22	chr6:24490400-24494600	Weak transcription	Fetal Intestine Small	intestine

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