Variant report

Variant	rs4622687
Chromosome Location	chr2:11840534-11840535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10164822	0.83[EUR][1000 genomes]
rs10182021	0.82[EUR][1000 genomes]
rs10206665	0.93[CEU][hapmap];0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs10209047	0.93[CEU][hapmap];0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs11886222	0.84[EUR][1000 genomes]
rs13386239	0.83[EUR][1000 genomes]
rs13387137	0.81[EUR][1000 genomes]
rs13390584	0.83[EUR][1000 genomes]
rs13398067	0.83[EUR][1000 genomes]
rs13407243	0.84[EUR][1000 genomes]
rs13407481	0.84[EUR][1000 genomes]
rs13420573	0.84[EUR][1000 genomes]
rs13426765	0.83[EUR][1000 genomes]
rs13431864	0.84[EUR][1000 genomes]
rs13432334	0.83[EUR][1000 genomes]
rs4296403	0.84[EUR][1000 genomes]
rs4564747	0.84[EUR][1000 genomes]
rs55773509	0.83[EUR][1000 genomes]
rs57055669	0.84[EUR][1000 genomes]
rs57281558	0.88[EUR][1000 genomes]
rs58196703	0.81[EUR][1000 genomes]
rs6432232	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6432233	0.93[CEU][hapmap];0.84[CHB][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66763856	0.84[EUR][1000 genomes]
rs6708244	0.93[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs6716051	0.88[EUR][1000 genomes]
rs6716192	0.88[EUR][1000 genomes]
rs6725991	0.83[EUR][1000 genomes]
rs6736015	0.93[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs6748533	0.83[EUR][1000 genomes]
rs7560325	0.83[EUR][1000 genomes]
rs7570592	0.84[EUR][1000 genomes]
rs7573725	0.83[EUR][1000 genomes]
rs7580112	0.84[EUR][1000 genomes]
rs7591517	0.83[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4622687	RRM2	cis	parietal	SCAN
rs4622687	LPIN1	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11829400-11841800	Weak transcription	Primary B cells from cord blood	blood
2	chr2:11833600-11841800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:11836800-11843200	Enhancers	Placenta	Placenta
4	chr2:11837400-11840800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:11837600-11840800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:11837800-11841200	Enhancers	Fetal Muscle Trunk	muscle
7	chr2:11837800-11843200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:11837800-11845400	Weak transcription	Pancreas	Pancrea
9	chr2:11837800-11848200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:11838000-11842400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:11838000-11842400	Weak transcription	Spleen	Spleen
12	chr2:11838000-11843000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:11838000-11843200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:11838200-11842000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:11838200-11843400	Weak transcription	HMEC	breast
16	chr2:11838400-11841400	Weak transcription	Fetal Thymus	thymus
17	chr2:11838400-11841600	Enhancers	Ovary	ovary
18	chr2:11838400-11844000	Weak transcription	Lung	lung
19	chr2:11838400-11845000	Weak transcription	Brain Anterior Caudate	brain
20	chr2:11838600-11843400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:11838600-11848000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:11838800-11841600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr2:11838800-11843400	Weak transcription	NH-A	brain
24	chr2:11839000-11841200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr2:11839000-11841200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:11839000-11841200	Enhancers	Psoas Muscle	Psoas
27	chr2:11839000-11841400	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr2:11839000-11841800	Weak transcription	Osteobl	bone
29	chr2:11839000-11842200	Weak transcription	K562	blood
30	chr2:11839000-11843200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:11839000-11843400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:11839000-11843400	Weak transcription	NHLF	lung
33	chr2:11839000-11843600	Weak transcription	NHEK	skin
34	chr2:11839200-11840800	Weak transcription	Brain Substantia Nigra	brain
35	chr2:11839200-11840800	Enhancers	HepG2	liver
36	chr2:11839200-11841000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:11839200-11841200	Weak transcription	Brain Angular Gyrus	brain
38	chr2:11839200-11841400	Weak transcription	Fetal Stomach	stomach
39	chr2:11839200-11842000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:11839200-11842000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr2:11839200-11842400	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:11839200-11843200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:11839200-11843600	Weak transcription	HSMMtube	muscle
44	chr2:11839400-11843200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:11839400-11843400	Weak transcription	HSMM	muscle
46	chr2:11839400-11843600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:11839800-11840800	Weak transcription	Esophagus	oesophagus
48	chr2:11840200-11842200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr2:11840200-11844000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:11840400-11840600	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast

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