Variant report

Variant	rs3770699
Chromosome Location	chr2:211304138-211304139
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10195342	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1027901	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1044708	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10804181	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10804182	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10804183	0.88[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11690895	0.85[ASN][1000 genomes]
rs11889228	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11894867	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11896108	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11900468	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12469589	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12473150	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12474078	0.81[TSI][hapmap]
rs12477237	0.83[EUR][1000 genomes]
rs1350463	0.86[EUR][1000 genomes]
rs1379838	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1812875	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2021214	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2042049	0.81[TSI][hapmap]
rs2287424	0.89[CEU][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2287425	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2287429	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2287430	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2287431	0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2287432	0.89[CEU][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2287433	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2370949	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2370956	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2887899	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35314871	0.89[EUR][1000 genomes]
rs3732055	0.81[TSI][hapmap]
rs3755184	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770689	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3770694	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770695	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3821136	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	0.89[CEU][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3851937	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3856339	0.89[CEU][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3863852	0.83[EUR][1000 genomes]
rs4102441	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41272663	0.83[ASN][1000 genomes]
rs4467201	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4609985	0.85[EUR][1000 genomes]
rs4673526	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4673528	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4673529	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6435568	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6435569	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6717228	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6745925	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6756422	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs725379	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72930503	0.91[ASN][1000 genomes]
rs72930539	0.85[ASN][1000 genomes]
rs7575005	0.83[ASN][1000 genomes]
rs7578688	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7595022	0.88[EUR][1000 genomes];0.91[ASN][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
rs3770699	CPS1	cis	cerebellum	SCAN
rs3770699	LANCL1	cis	cerebellum	SCAN
rs3770699	CRYGB	cis	cerebellum	SCAN
rs3770699	UNC80	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211292400-211323000	Weak transcription	Fetal Brain Male	brain
2	chr2:211293000-211305800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:211293200-211307400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr2:211293200-211307800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:211293200-211311600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:211293800-211335400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:211294800-211306200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:211294800-211306400	Strong transcription	Dnd41	blood
9	chr2:211294800-211322200	Weak transcription	K562	blood
10	chr2:211294800-211333200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:211295000-211306600	Strong transcription	Brain Cingulate Gyrus	brain
12	chr2:211295000-211307400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:211295000-211330400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:211295000-211336000	Weak transcription	Colonic Mucosa	Colon
15	chr2:211295000-211340600	Weak transcription	HUVEC	blood vessel
16	chr2:211295400-211309200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:211295600-211305200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:211295600-211306200	Strong transcription	Adipose Nuclei	Adipose
19	chr2:211295600-211306600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:211295600-211307800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:211295600-211308000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr2:211295800-211305200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:211295800-211306000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:211295800-211306000	Strong transcription	HSMMtube	muscle
25	chr2:211295800-211307200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:211295800-211307400	Strong transcription	Fetal Thymus	thymus
27	chr2:211295800-211307600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:211296000-211305600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:211296000-211305800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:211296000-211306000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:211296000-211307600	Strong transcription	Primary B cells from cord blood	blood
32	chr2:211296000-211309000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:211296000-211340200	Weak transcription	Small Intestine	intestine
34	chr2:211296400-211304600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:211296400-211305400	Strong transcription	Osteobl	bone
36	chr2:211296400-211309200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:211296400-211341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr2:211296600-211306600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:211297200-211307000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:211297400-211306000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr2:211297400-211309000	Strong transcription	Brain Angular Gyrus	brain
42	chr2:211297400-211321400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:211297800-211336200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:211298000-211306400	Strong transcription	Brain Anterior Caudate	brain
45	chr2:211299000-211304200	Strong transcription	HSMM	muscle
46	chr2:211299000-211304600	Strong transcription	Brain Substantia Nigra	brain
47	chr2:211299200-211304600	Weak transcription	Fetal Heart	heart
48	chr2:211299400-211305400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:211299400-211307000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr2:211299400-211322600	Weak transcription	H9 Cell Line	embryonic stem cell

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