Variant report

Variant	rs2744550
Chromosome Location	chr6:24564544-24564545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24525412..24526236-chr6:24563796..24564629,3	MCF-7	breast:
2	chr6:24555919..24558537-chr6:24563270..24565102,2	MCF-7	breast:
3	chr6:24550879..24552462-chr6:24563230..24564931,2	K562	blood:
4	chr6:24563668..24565517-chr6:24568197..24570013,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs16889633	1.00[CHD][hapmap]
rs1772256	1.00[CHD][hapmap]
rs1923187	1.00[CHD][hapmap]
rs2744548	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2744549	1.00[ASW][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2744552	0.92[AFR][1000 genomes]
rs2744558	0.87[ASW][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2744559	1.00[CHD][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2744561	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2744562	0.87[EUR][1000 genomes]
rs2760155	0.87[EUR][1000 genomes]
rs2760156	0.87[EUR][1000 genomes]
rs2760160	0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2760161	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2760162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2760163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2760164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2760180	0.86[EUR][1000 genomes]
rs2817191	1.00[ASW][hapmap];1.00[CHD][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]
rs2817192	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2817193	1.00[EUR][1000 genomes]
rs2817194	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2817195	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28360750	0.86[EUR][1000 genomes]
rs4472344	1.00[CHD][hapmap]
rs6921275	0.86[EUR][1000 genomes]
rs7740941	0.86[EUR][1000 genomes]
rs7744621	1.00[CHD][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7744939	1.00[CHD][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7749794	1.00[CHD][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7751846	1.00[CHD][hapmap]
rs7752186	1.00[CHD][hapmap]
rs7752603	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs7760171	1.00[CHD][hapmap]
rs7764860	1.00[CHD][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7768735	0.86[EUR][1000 genomes]
rs7770041	1.00[CHD][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7772115	1.00[CHD][hapmap]
rs7772540	1.00[CHD][hapmap]
rs7773122	0.86[EUR][1000 genomes]
rs7773357	0.86[EUR][1000 genomes]
rs793656	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1020653	chr6:24557870-24638244	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
2	chr6:24535200-24566600	Weak transcription	Brain Germinal Matrix	brain
3	chr6:24535200-24591200	Weak transcription	Fetal Brain Male	brain
4	chr6:24535600-24583400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:24539200-24583200	Weak transcription	Fetal Intestine Small	intestine
6	chr6:24548400-24583400	Weak transcription	A549	lung
7	chr6:24550200-24566400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:24552600-24568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:24559600-24577600	Weak transcription	Pancreas	Pancrea
10	chr6:24562400-24583400	Weak transcription	Right Atrium	heart
11	chr6:24563200-24565200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:24563200-24565200	Strong transcription	Fetal Brain Female	brain
13	chr6:24563400-24565000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:24563600-24564800	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr6:24564000-24564800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:24564400-24564600	Flanking Bivalent TSS/Enh	HepG2	liver
17	chr6:24564400-24583400	Weak transcription	Brain Angular Gyrus	brain
18	chr6:24564400-24583400	Weak transcription	Brain Anterior Caudate	brain

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