Variant report

Variant	rs2292887
Chromosome Location	chr2:86705565-86705566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86704223..86708236-chr2:86709425..86713459,5	K562	blood:
2	chr2:86703571..86706359-chr2:86706716..86708638,2	MCF-7	breast:
3	chr2:86667473..86669987-chr2:86705079..86707009,2	K562	blood:
4	chr2:86704538..86706157-chr2:86711793..86713766,2	K562	blood:

Variant related genes	Relation type
ENSG00000115548	Chromatin interaction

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

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

rs_ID	r²[population]
rs1015117	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10169091	0.87[JPT][hapmap]
rs10180036	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10184879	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs10187880	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs1020306	0.81[EUR][1000 genomes]
rs1105865	0.82[CHB][hapmap]
rs11127034	0.90[ASN][1000 genomes]
rs11127045	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1137684	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11684230	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12613282	0.93[CEU][hapmap];1.00[YRI][hapmap]
rs12614447	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12615285	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12617075	0.85[CHB][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes]
rs12623509	0.93[CEU][hapmap]
rs12714184	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12714186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12714198	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs12987172	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13015620	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs13034615	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[TSI][hapmap]
rs13383096	0.81[AMR][1000 genomes]
rs1465813	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1518807	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1629293	0.81[GIH][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap]
rs2113607	0.85[CHB][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs2241803	1.00[ASW][hapmap];0.93[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2367574	0.88[EUR][1000 genomes]
rs308910	0.82[TSI][hapmap]
rs308914	0.81[GIH][hapmap];0.87[MKK][hapmap];0.80[TSI][hapmap]
rs3201448	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3731812	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3755002	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3770058	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs422240	0.88[MKK][hapmap];0.82[TSI][hapmap]
rs4832282	0.85[CHB][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes]
rs4832297	0.96[CEU][hapmap]
rs4832300	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4832304	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs62150269	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6547685	0.82[CHB][hapmap]
rs6725080	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6738663	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6750226	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6751871	0.82[CHB][hapmap]
rs6755760	0.82[CHB][hapmap]
rs7369138	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs766285	0.81[JPT][hapmap]
rs9284788	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs958561	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2292887	VPS24	cis	parietal	SCAN
rs2292887	MRPL35	cis	parietal	SCAN
rs2292887	PTCD3	cis	cerebellum	SCAN
rs2292887	RNF103	cis	cerebellum	SCAN
rs2292887	POLR1A	cis	cerebellum	SCAN
rs2292887	MAT2A	cis	parietal	SCAN
rs2292887	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs2292887	IMMT	cis	cerebellum	SCAN

Chromatin state (count:125 , 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	chr2:86671600-86719800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr2:86671600-86723600	Strong transcription	Fetal Thymus	thymus
6	chr2:86671600-86726000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:86671800-86726600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:86672600-86721200	Strong transcription	Fetal Intestine Large	intestine
9	chr2:86672600-86724200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:86674200-86726800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:86674600-86721400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:86676400-86722600	Strong transcription	GM12878-XiMat	blood
13	chr2:86676600-86721600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:86676600-86727200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:86677200-86708200	Strong transcription	HepG2	liver
16	chr2:86677200-86709200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:86679400-86708000	Strong transcription	Primary hematopoietic stem cells	blood
18	chr2:86679600-86721400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:86679600-86721800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:86680200-86722200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:86681000-86720800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr2:86681600-86722600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:86681600-86727000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr2:86682000-86707000	Strong transcription	Adipose Nuclei	Adipose
26	chr2:86682000-86718600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung
29	chr2:86683000-86709600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr2:86683800-86708400	Strong transcription	HMEC	breast
31	chr2:86684000-86720800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:86684000-86726000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr2:86685400-86707000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:86690200-86723200	Strong transcription	Primary B cells from cord blood	blood
35	chr2:86693800-86708000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:86694000-86707000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:86694000-86709000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:86696000-86712000	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:86696800-86720600	Strong transcription	Hela-S3	cervix
41	chr2:86697000-86719200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:86697000-86719800	Strong transcription	Thymus	Thymus
43	chr2:86697000-86721200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:86697000-86721400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:86697200-86724600	Strong transcription	Dnd41	blood
46	chr2:86697400-86721000	Strong transcription	HUVEC	blood vessel
47	chr2:86697400-86721600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:86697600-86709600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:86697600-86723000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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