Variant report

Variant	rs11840819
Chromosome Location	chr13:49110358-49110359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr13:49109930-49110390	HL-60	blood:	n/a	chr13:49110184-49110197

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:49106158..49108541-chr13:49108790..49110495,3	MCF-7	breast:
2	chr13:49066611..49068640-chr13:49109676..49111240,2	MCF-7	breast:
3	chr13:49109335..49111228-chr13:49113801..49116613,2	MCF-7	breast:
4	chr13:49107018..49108572-chr13:49108963..49111065,3	MCF-7	breast:
5	chr13:49107619..49110446-chr13:49111219..49113821,2	MCF-7	breast:
6	chr13:49109125..49111040-chr13:49114592..49116444,2	K562	blood:
7	chr13:49102666..49106800-chr13:49108921..49111572,3	MCF-7	breast:

No data

Variant related genes	Relation type
RCBTB2	TF binding region
ENSG00000136161	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10076	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs10467381	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11842402	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11842662	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13378245	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17071917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17071960	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs174854	0.95[AMR][1000 genomes]
rs198565	0.95[AMR][1000 genomes]
rs198573	0.95[AMR][1000 genomes]
rs198581	0.90[AMR][1000 genomes]
rs198583	0.95[AMR][1000 genomes]
rs198587	0.95[AMR][1000 genomes]
rs2984828	0.95[AMR][1000 genomes]
rs3020646	0.95[AMR][1000 genomes]
rs7322110	0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7332631	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7984270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316384	0.82[AMR][1000 genomes]
rs9316387	0.82[AMR][1000 genomes]
rs9316390	0.83[AMR][1000 genomes]
rs9316391	0.83[AMR][1000 genomes]
rs9316392	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9316403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9332025	0.83[AMR][1000 genomes]
rs9332036	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332050	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9332053	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332066	0.95[AMR][1000 genomes]
rs9591167	0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9591170	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591171	0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9591174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591175	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595913	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9595914	0.82[AMR][1000 genomes]
rs9595917	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9595930	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595936	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49107200-49110800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr13:49107800-49110400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr13:49107800-49110400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:49107800-49110800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr13:49107800-49116200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:49107800-49116200	Weak transcription	Left Ventricle	heart
7	chr13:49107800-49116200	Weak transcription	Right Atrium	heart
8	chr13:49107800-49116200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr13:49107800-49116400	Weak transcription	Lung	lung
10	chr13:49107800-49116800	Weak transcription	Pancreas	Pancrea
11	chr13:49108000-49116600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr13:49108200-49111000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:49108400-49110600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr13:49108400-49116400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr13:49108600-49111400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr13:49110200-49112400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links