Variant report

Variant	rs2367575
Chromosome Location	chr2:86720841-86720842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86720517..86722121-chr2:86723212..86725706,2	K562	blood:
2	chr2:86707439..86709100-chr2:86718829..86721673,2	K562	blood:
3	chr2:86716552..86718952-chr2:86720243..86722913,2	MCF-7	breast:
4	chr2:86720341..86722407-chr2:86724543..86726613,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10185085	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1036940	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];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11127040	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11127042	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11127047	0.83[GIH][hapmap]
rs1116326	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11690696	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11693352	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11900816	0.84[CEU][hapmap]
rs11903855	1.00[CHB][hapmap]
rs12475983	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12476666	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12714185	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12714187	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12995117	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];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1468039	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1518811	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2030259	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2044230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2139150	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs218060	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs308901	0.87[CHD][hapmap]
rs308907	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap]
rs308911	0.82[GIH][hapmap]
rs308913	1.00[JPT][hapmap]
rs396354	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs433655	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4832284	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4832285	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4832287	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4832288	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4832289	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832290	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832293	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832298	0.80[ASN][1000 genomes]
rs6547688	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6547689	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6547690	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6547700	0.87[CHD][hapmap]
rs6710124	1.00[CHB][hapmap]
rs6714826	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];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714957	0.80[ASN][1000 genomes]
rs6742018	1.00[JPT][hapmap]
rs683139	0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs7557796	0.83[GIH][hapmap]
rs7574389	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7598058	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs950780	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs966477	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2367575	IMMT	cis	lymphoblastoid	seeQTL
rs2367575	MAT2A	cis	parietal	SCAN
rs2367575	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs2367575	RNF103	cis	cerebellum	SCAN
rs2367575	PTCD3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86671000-86725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:86671400-86722600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:86671400-86725600	Strong transcription	A549	lung
4	chr2:86671600-86723600	Strong transcription	Fetal Thymus	thymus
5	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr2:86672600-86721200	Strong transcription	Fetal Intestine Large	intestine
8	chr2:86672600-86724200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:86674600-86721400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:86676400-86722600	Strong transcription	GM12878-XiMat	blood
12	chr2:86676600-86721600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:86679600-86721400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:86679600-86721800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:86680200-86722200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:86681600-86722600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung
22	chr2:86684000-86726000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:86690200-86723200	Strong transcription	Primary B cells from cord blood	blood
24	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr2:86697000-86721200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:86697000-86721400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:86697200-86724600	Strong transcription	Dnd41	blood
28	chr2:86697400-86721000	Strong transcription	HUVEC	blood vessel
29	chr2:86697400-86721600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:86697600-86723000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:86697800-86721600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:86697800-86728800	Strong transcription	Primary T cells from cord blood	blood
34	chr2:86699400-86727000	Strong transcription	Placenta	Placenta
35	chr2:86701000-86725600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:86702400-86721000	Strong transcription	Fetal Brain Female	brain
37	chr2:86703800-86721000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:86703800-86721200	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:86704600-86723000	Strong transcription	Fetal Kidney	kidney
40	chr2:86704800-86721000	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr2:86704800-86726400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:86704800-86726600	Strong transcription	NHDF-Ad	bronchial
43	chr2:86705000-86721400	Strong transcription	Osteobl	bone
44	chr2:86706000-86721400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:86706000-86724400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:86708800-86721600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr2:86708800-86726600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:86709200-86726600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:86709800-86721400	Strong transcription	HMEC	breast

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