Variant report

Variant	rs3821136
Chromosome Location	chr2:211299687-211299688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10195342	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1027901	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044708	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804181	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10804182	0.86[EUR][1000 genomes]
rs10804183	0.81[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs11889228	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs11894867	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11896108	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11900468	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12469589	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12473150	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12477237	0.82[EUR][1000 genomes]
rs1350463	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1379838	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1812875	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2021214	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2287424	0.81[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2287425	0.86[EUR][1000 genomes]
rs2287429	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs2287430	0.87[EUR][1000 genomes]
rs2287432	0.81[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2287433	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2370949	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs2370956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887899	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs35314871	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755184	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs3770689	0.87[EUR][1000 genomes]
rs3770694	0.86[EUR][1000 genomes]
rs3770695	0.87[EUR][1000 genomes]
rs3770699	0.87[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3845633	0.81[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs3851937	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856339	0.81[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs3863852	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4102441	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41272663	0.99[ASN][1000 genomes]
rs4467201	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4609985	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4673526	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4673528	0.81[EUR][1000 genomes]
rs4673529	0.84[EUR][1000 genomes]
rs6435568	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435569	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6717228	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6745925	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6756422	0.87[EUR][1000 genomes]
rs725379	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs7575005	0.99[ASN][1000 genomes]
rs7578688	0.86[EUR][1000 genomes]
rs7595022	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012567	chr2:211087588-211315554	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv875767	chr2:211119233-211334647	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv3147	chr2:211281479-211326844	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3821136	CPS1	cis	cerebellum	SCAN
rs3821136	CPS1	cis	parietal	SCAN
rs3821136	LANCL1	cis	cerebellum	SCAN
rs3821136	CRYGB	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211291600-211300800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:211292400-211323000	Weak transcription	Fetal Brain Male	brain
3	chr2:211293000-211305800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:211293200-211307400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr2:211293200-211307800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:211293200-211311600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:211293800-211335400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:211294200-211301400	Strong transcription	Primary T cells from cord blood	blood
9	chr2:211294400-211303400	Weak transcription	NHLF	lung
10	chr2:211294800-211306200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:211294800-211306400	Strong transcription	Dnd41	blood
12	chr2:211294800-211322200	Weak transcription	K562	blood
13	chr2:211294800-211333200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:211295000-211306600	Strong transcription	Brain Cingulate Gyrus	brain
15	chr2:211295000-211307400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:211295000-211330400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:211295000-211336000	Weak transcription	Colonic Mucosa	Colon
18	chr2:211295000-211340600	Weak transcription	HUVEC	blood vessel
19	chr2:211295400-211309200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:211295600-211301800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr2:211295600-211302000	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr2:211295600-211302400	Strong transcription	Primary hematopoietic stem cells	blood
23	chr2:211295600-211302400	Strong transcription	Brain Hippocampus Middle	brain
24	chr2:211295600-211305200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:211295600-211306200	Strong transcription	Adipose Nuclei	Adipose
26	chr2:211295600-211306600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:211295600-211307800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:211295600-211308000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr2:211295800-211301600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:211295800-211302600	Strong transcription	Liver	Liver
31	chr2:211295800-211302600	Strong transcription	Fetal Brain Female	brain
32	chr2:211295800-211305200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:211295800-211306000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:211295800-211306000	Strong transcription	HSMMtube	muscle
35	chr2:211295800-211307200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:211295800-211307400	Strong transcription	Fetal Thymus	thymus
37	chr2:211295800-211307600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:211296000-211299800	Strong transcription	GM12878-XiMat	blood
39	chr2:211296000-211300200	Strong transcription	NHDF-Ad	bronchial
40	chr2:211296000-211301400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr2:211296000-211302000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:211296000-211302200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:211296000-211302400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:211296000-211302400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr2:211296000-211302400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr2:211296000-211302600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:211296000-211302600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:211296000-211302800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:211296000-211302800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:211296000-211305600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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