Variant report

Variant	rs12714187
Chromosome Location	chr2:86691250-86691251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86676103..86683651-chr2:86688314..86691319,7	K562	blood:
2	chr2:86668149..86671762-chr2:86690412..86696565,6	K562	blood:

Variant related genes	Relation type
ENSG00000115548	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];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1036940	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11127040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11127042	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[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1116326	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11690696	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11693352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11903855	1.00[CHB][hapmap]
rs12475983	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12476666	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12714185	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];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1468039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1518811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2030259	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2139150	1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs218060	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2367575	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[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	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832285	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[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832287	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832288	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4832289	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]
rs4832290	0.95[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832293	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832294	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6547688	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6547689	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6547690	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs6742018	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs683139	0.87[CHD][hapmap]
rs7574389	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[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7598058	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs950780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs966477	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[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
rs12714187	ST3GAL5	cis	parietal	SCAN
rs12714187	RNF103	cis	cerebellum	SCAN
rs12714187	KDM3A	cis	parietal	SCAN
rs12714187	IMMT	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86670400-86693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:86671000-86725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:86671400-86722600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:86671400-86725600	Strong transcription	A549	lung
5	chr2:86671600-86695400	Strong transcription	HSMM	muscle
6	chr2:86671600-86719800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr2:86671600-86723600	Strong transcription	Fetal Thymus	thymus
8	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr2:86672600-86721200	Strong transcription	Fetal Intestine Large	intestine
11	chr2:86672600-86724200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:86674600-86721400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:86674800-86695000	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr2:86675400-86694600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:86675600-86692000	Strong transcription	Dnd41	blood
17	chr2:86676400-86693600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:86676400-86722600	Strong transcription	GM12878-XiMat	blood
19	chr2:86676600-86695600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:86676600-86721600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:86676800-86698200	Strong transcription	Placenta	Placenta
23	chr2:86676800-86701000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:86676800-86703800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:86677000-86692000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:86677000-86705200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:86677200-86708200	Strong transcription	HepG2	liver
28	chr2:86677200-86709200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:86677800-86691600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:86677800-86693200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:86678000-86693200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:86679400-86708000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr2:86679600-86721400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:86679600-86721800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr2:86680200-86722200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:86681000-86720800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr2:86681600-86691600	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:86681600-86699600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:86681600-86722600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr2:86681800-86699000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:86681800-86702600	Strong transcription	NHDF-Ad	bronchial
44	chr2:86681800-86703600	Strong transcription	Liver	Liver
45	chr2:86682000-86691800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:86682000-86702400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:86682000-86707000	Strong transcription	Adipose Nuclei	Adipose
48	chr2:86682000-86718600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung

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