Variant report

Variant	rs4640359
Chromosome Location	chr2:11853964-11853965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11850883..11854568-chr2:11860179..11862646,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10929766	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11684640	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11684644	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11687567	1.00[AFR][1000 genomes]
rs11691889	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11893735	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12469060	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12470427	0.81[AMR][1000 genomes]
rs3923671	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3924929	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4366872	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4371339	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4517949	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4614906	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4640362	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55864809	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56387825	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58026116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59341236	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60118851	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7587266	0.82[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv469449	chr2:11808654-11854012	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv580972	chr2:11808654-11854012	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11844200-11854200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:11844600-11856400	Weak transcription	Psoas Muscle	Psoas
3	chr2:11848800-11854600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:11848800-11855400	Weak transcription	Pancreas	Pancrea
5	chr2:11849000-11854400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:11850600-11856400	Weak transcription	Hela-S3	cervix
7	chr2:11850800-11856200	Weak transcription	Right Atrium	heart
8	chr2:11851400-11856600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:11851400-11856600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:11851600-11855600	Weak transcription	Liver	Liver
11	chr2:11851800-11856600	Weak transcription	Fetal Lung	lung
12	chr2:11851800-11856800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:11852000-11859200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:11852200-11858600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:11852400-11858800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:11852600-11856000	Weak transcription	Adipose Nuclei	Adipose
17	chr2:11852600-11856200	Weak transcription	Ovary	ovary
18	chr2:11852600-11859400	Weak transcription	Brain Substantia Nigra	brain
19	chr2:11852600-11860600	Weak transcription	Esophagus	oesophagus
20	chr2:11852800-11858800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:11852800-11859200	Weak transcription	Brain Angular Gyrus	brain
22	chr2:11853000-11856600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:11853000-11856600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr2:11853000-11856800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr2:11853200-11855400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:11853200-11856200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:11853200-11856200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:11853400-11856800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:11853800-11854000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:11853800-11854600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links