Variant report

Variant	rs12474078
Chromosome Location	chr2:211330342-211330343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:211328360..211331054-chr2:211338768..211341669,2	K562	blood:

Variant related genes	Relation type
ENSG00000115365	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10804183	0.91[GIH][hapmap];0.83[TSI][hapmap]
rs10932334	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11895784	0.81[CEU][hapmap]
rs12464878	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623942	0.99[ASN][1000 genomes]
rs1396954	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17552879	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2042049	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[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	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287419	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287420	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.87[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]
rs2287424	0.91[GIH][hapmap];0.83[TSI][hapmap]
rs2287432	0.89[GIH][hapmap];0.83[TSI][hapmap]
rs2370948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732055	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755182	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770685	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3770687	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770690	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]
rs3770691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770699	0.81[TSI][hapmap]
rs3845633	0.89[GIH][hapmap];0.81[TSI][hapmap]
rs3856339	0.89[GIH][hapmap];0.83[TSI][hapmap]
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];0.99[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];0.86[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];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856346	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3856347	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856348	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3856349	0.96[AMR][1000 genomes];0.85[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];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4673532	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4673533	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62203668	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62203675	0.97[AMR][1000 genomes];0.84[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12474078	CPS1	cis	Adipose Subcutaneous	GTEx
rs12474078	LANCL1	Cis_1M	lymphoblastoid	RTeQTL
rs12474078	CPS1	cis	Artery Tibial	GTEx
rs12474078	LANCL1	cis	parietal	SCAN
rs12474078	LANCL1	cis	cerebellum	SCAN
rs12474078	CPS1	cis	lung	GTEx
rs12474078	CPS1	cis	parietal	SCAN
rs12474078	CPS1	cis	cerebellum	SCAN

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	chr2:211295000-211330400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:211295000-211336000	Weak transcription	Colonic Mucosa	Colon
5	chr2:211295000-211340600	Weak transcription	HUVEC	blood vessel
6	chr2:211296000-211340200	Weak transcription	Small Intestine	intestine
7	chr2:211296400-211341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:211297800-211336200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:211301200-211340200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:211301200-211340600	Weak transcription	Fetal Intestine Small	intestine
11	chr2:211301200-211340800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:211301400-211330800	Weak transcription	Right Ventricle	heart
13	chr2:211301400-211334400	Weak transcription	NHEK	skin
14	chr2:211301400-211336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:211308000-211332400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:211315400-211340000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:211315600-211337800	Strong transcription	Fetal Thymus	thymus
18	chr2:211315600-211339600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:211315800-211337200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:211315800-211337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:211316000-211338000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:211316200-211337800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:211316200-211337800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:211316600-211339000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:211316800-211338800	Strong transcription	Dnd41	blood
26	chr2:211318000-211337800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr2:211320000-211331000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:211320000-211331200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:211320000-211333200	Weak transcription	NHLF	lung
30	chr2:211321000-211331400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:211321000-211334200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr2:211321200-211337600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:211322400-211340400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:211322600-211340400	Weak transcription	K562	blood
35	chr2:211323200-211330800	Weak transcription	Spleen	Spleen
36	chr2:211323200-211330800	Weak transcription	Osteobl	bone
37	chr2:211323200-211333200	Weak transcription	Pancreas	Pancrea
38	chr2:211323400-211330800	Weak transcription	Fetal Stomach	stomach
39	chr2:211323400-211330800	Weak transcription	Ovary	ovary
40	chr2:211323400-211331000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:211323400-211331200	Weak transcription	Lung	lung
42	chr2:211323400-211331600	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:211323400-211331800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:211323400-211331800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:211323400-211334000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:211323400-211336000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:211323400-211340200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr2:211323600-211330800	Weak transcription	Placenta	Placenta
49	chr2:211324200-211333000	Weak transcription	Fetal Heart	heart
50	chr2:211324200-211336000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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