Variant report

Variant	rs3770690
Chromosome Location	chr2:211333049-211333050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:211332522..211338097-chr2:211338673..211343444,12	K562	blood:
2	chr2:211331262..211333648-chr2:211337873..211339942,2	MCF-7	breast:
3	chr2:211331048..211333465-chr2:211338330..211339916,2	MCF-7	breast:
4	chr2:211331221..211336571-chr2:211337651..211341435,6	K562	blood:

Variant related genes	Relation type
ENSG00000021826	Chromatin interaction
ENSG00000115365	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10932334	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12464878	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12474078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623942	0.99[ASN][1000 genomes]
rs1396954	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17552879	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2042049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287417	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287418	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287419	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287420	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2287422	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2370948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755182	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3770687	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3856343	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856344	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856345	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856346	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856347	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856348	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856349	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4672575	0.95[ASN][1000 genomes]
rs4672577	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4673530	0.97[ASN][1000 genomes]
rs4673531	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4673532	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4673533	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62203668	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203669	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203670	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62203672	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62203673	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62203674	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62203675	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6727682	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7569252	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3770690	CPS1	cis	Adipose Subcutaneous	GTEx
rs3770690	CPS1	cis	lung	GTEx
rs3770690	LANCL1	Cis_1M	lymphoblastoid	RTeQTL
rs3770690	CPS1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211293800-211335400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:211294800-211333200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:211295000-211336000	Weak transcription	Colonic Mucosa	Colon
4	chr2:211295000-211340600	Weak transcription	HUVEC	blood vessel
5	chr2:211296000-211340200	Weak transcription	Small Intestine	intestine
6	chr2:211296400-211341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:211297800-211336200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:211301200-211340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:211301200-211340600	Weak transcription	Fetal Intestine Small	intestine
10	chr2:211301200-211340800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:211301400-211334400	Weak transcription	NHEK	skin
12	chr2:211301400-211336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:211315400-211340000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:211315600-211337800	Strong transcription	Fetal Thymus	thymus
15	chr2:211315600-211339600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:211315800-211337200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:211315800-211337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:211316000-211338000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:211316200-211337800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:211316200-211337800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:211316600-211339000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:211316800-211338800	Strong transcription	Dnd41	blood
23	chr2:211318000-211337800	Strong transcription	Stomach Smooth Muscle	stomach
24	chr2:211320000-211333200	Weak transcription	NHLF	lung
25	chr2:211321000-211334200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:211321200-211337600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:211322400-211340400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:211322600-211340400	Weak transcription	K562	blood
29	chr2:211323200-211333200	Weak transcription	Pancreas	Pancrea
30	chr2:211323400-211334000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:211323400-211336000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:211323400-211340200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:211324200-211336000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:211324800-211339000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:211325200-211333200	Weak transcription	Fetal Brain Male	brain
36	chr2:211325800-211340800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:211326200-211333200	Weak transcription	Esophagus	oesophagus
38	chr2:211326800-211333200	Weak transcription	HSMM	muscle
39	chr2:211326800-211338800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:211326800-211339800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:211327000-211333200	Weak transcription	NHDF-Ad	bronchial
42	chr2:211327200-211338000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:211327400-211339000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:211327600-211339000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:211328000-211334200	Strong transcription	Brain Germinal Matrix	brain
46	chr2:211328200-211337800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:211328600-211334000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:211328600-211337000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:211329400-211334400	Strong transcription	Fetal Brain Female	brain
50	chr2:211329400-211336600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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