Variant report

Variant	rs4832290
Chromosome Location	chr2:86707504-86707505
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	FOXA2	chr2:86707313-86707599	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:86707194-86707678	GM12878	blood:	n/a	n/a
3	FOXA1	chr2:86707237-86707725	T-47D	breast:	n/a	chr2:86707462-86707477
4	FOXA1	chr2:86707303-86707659	T-47D	breast:	n/a	chr2:86707462-86707477
5	CTCF	chr2:86707460-86707610	GM12869	blood:	n/a	n/a
6	FOXA1	chr2:86707314-86707687	HepG2	liver:	n/a	chr2:86707462-86707477
7	POLR2A	chr2:86707428-86707628	HepG2	liver:	n/a	n/a
8	FOXA1	chr2:86707302-86707608	HepG2	liver:	n/a	chr2:86707462-86707477

No.	Distal block	Cell Line	Cell type
1	chr2:86704223..86708236-chr2:86709425..86713459,5	K562	blood:
2	chr2:86707439..86709100-chr2:86718829..86721673,2	K562	blood:
3	chr2:86703571..86706359-chr2:86706716..86708638,2	MCF-7	breast:

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

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10185085	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];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1036940	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11127040	0.95[CEU][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11127042	0.91[ASW][hapmap];0.95[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11127047	0.83[GIH][hapmap]
rs1116326	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11690696	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11693352	0.91[ASW][hapmap];0.95[CEU][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11900816	0.84[CEU][hapmap]
rs12475983	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12476666	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12714185	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]
rs12714187	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]
rs12995117	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1468039	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1518811	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2030259	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]
rs2044230	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2139150	0.91[ASW][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2367575	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs308907	0.82[GIH][hapmap]
rs308911	0.82[GIH][hapmap]
rs433655	0.82[GIH][hapmap];0.86[ASN][1000 genomes]
rs4832284	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4832285	0.91[ASW][hapmap];0.95[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4832287	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4832288	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4832289	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	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832294	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832298	0.80[ASN][1000 genomes]
rs6547688	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6547689	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6547690	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6714826	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714957	0.80[ASN][1000 genomes]
rs683139	0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs7557796	0.83[GIH][hapmap]
rs7574389	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];0.81[ASN][1000 genomes]
rs7598058	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs950780	0.95[CEU][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs966477	0.87[CHD][hapmap];0.91[GIH][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
rs4832290	MAT2A	cis	parietal	SCAN
rs4832290	PTCD3	cis	cerebellum	SCAN
rs4832290	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs4832290	IMMT	cis	lymphoblastoid	seeQTL
rs4832290	RNF103	cis	cerebellum	SCAN

Chromatin state (count:126 , 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	chr2:86682000-86718600	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr2:86682000-86726600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:86682200-86726200	Strong transcription	Fetal Lung	lung
28	chr2:86683000-86709600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:86683800-86708400	Strong transcription	HMEC	breast
30	chr2:86684000-86720800	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:86684000-86726000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr2:86690200-86723200	Strong transcription	Primary B cells from cord blood	blood
33	chr2:86693800-86708000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr2:86694000-86709000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:86696000-86712000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:86696000-86727000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:86696800-86720600	Strong transcription	Hela-S3	cervix
38	chr2:86697000-86719200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr2:86697000-86719800	Strong transcription	Thymus	Thymus
40	chr2:86697000-86721200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr2:86697000-86721400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:86697200-86724600	Strong transcription	Dnd41	blood
43	chr2:86697400-86721000	Strong transcription	HUVEC	blood vessel
44	chr2:86697400-86721600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:86697600-86709600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:86697600-86723000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:86697600-86727200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:86697800-86714800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
49	chr2:86697800-86721600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:86697800-86728800	Strong transcription	Primary T cells from cord blood	blood

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