Variant report

Variant	rs12714185
Chromosome Location	chr2:86678737-86678738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:86678462-86682101	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:86678168..86680549-chr2:86693508..86696096,2	K562	blood:
2	chr2:86676152..86678942-chr2:86849820..86852421,2	MCF-7	breast:
3	chr2:86677483..86680429-chr2:86702820..86704627,2	K562	blood:

Variant related genes	Relation type
KDM3A	TF binding region
ENSG00000249884	Chromatin interaction
ENSG00000115548	Chromatin interaction
ENSG00000239305	Chromatin interaction

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

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

rs_ID	r²[population]
rs10185085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036940	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11127040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1116326	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11690696	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11693352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11903855	1.00[CHB][hapmap]
rs12475983	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12476666	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12995117	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1468039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1518811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2030259	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2044230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2139150	1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs218060	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2367575	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs308901	0.87[CHD][hapmap]
rs308907	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs308913	1.00[JPT][hapmap]
rs396354	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs433655	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4832284	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832287	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832288	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832289	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832290	0.95[CEU][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832293	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832294	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6547688	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547689	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547690	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547700	0.87[CHD][hapmap]
rs6710124	1.00[CHB][hapmap]
rs6714826	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs6742018	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs683139	0.87[CHD][hapmap]
rs7574389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598058	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966477	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12714185	ST3GAL5	cis	parietal	SCAN
rs12714185	RNF103	cis	cerebellum	SCAN
rs12714185	IMMT	cis	lymphoblastoid	seeQTL
rs12714185	KDM3A	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86669800-86679200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:86670000-86684200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:86670400-86693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:86670800-86681000	Weak transcription	Stomach Mucosa	stomach
5	chr2:86670800-86684200	Weak transcription	Colonic Mucosa	Colon
6	chr2:86671000-86725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:86671200-86689400	Strong transcription	Primary B cells from cord blood	blood
8	chr2:86671400-86684200	Weak transcription	Gastric	stomach
9	chr2:86671400-86685600	Weak transcription	Esophagus	oesophagus
10	chr2:86671400-86687800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:86671400-86722600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:86671400-86725600	Strong transcription	A549	lung
13	chr2:86671600-86680800	Weak transcription	Fetal Brain Male	brain
14	chr2:86671600-86695400	Strong transcription	HSMM	muscle
15	chr2:86671600-86719800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:86671600-86723600	Strong transcription	Fetal Thymus	thymus
17	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:86671800-86680400	Weak transcription	Right Atrium	heart
19	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:86672000-86681400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:86672600-86721200	Strong transcription	Fetal Intestine Large	intestine
22	chr2:86672600-86724200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:86672800-86678800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:86672800-86680400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:86672800-86680600	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr2:86674000-86685200	Weak transcription	Pancreas	Pancrea
27	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:86674600-86721400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:86674800-86680200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr2:86674800-86695000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr2:86675000-86680400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:86675000-86682600	Strong transcription	K562	blood
33	chr2:86675200-86680600	Strong transcription	Brain Cingulate Gyrus	brain
34	chr2:86675400-86678800	Weak transcription	Psoas Muscle	Psoas
35	chr2:86675400-86694600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:86675600-86692000	Strong transcription	Dnd41	blood
37	chr2:86675800-86680000	Strong transcription	HUVEC	blood vessel
38	chr2:86676000-86680800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:86676200-86682600	Strong transcription	Primary T cells from cord blood	blood
40	chr2:86676400-86679200	Strong transcription	NHEK	skin
41	chr2:86676400-86680400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:86676400-86680400	Strong transcription	HMEC	breast
43	chr2:86676400-86680600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:86676400-86681200	Strong transcription	Fetal Muscle Leg	muscle
45	chr2:86676400-86683200	Strong transcription	Thymus	Thymus
46	chr2:86676400-86693600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:86676400-86722600	Strong transcription	GM12878-XiMat	blood
48	chr2:86676600-86678800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:86676600-86680400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:86676600-86680600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links