Variant report

Variant	rs2252032
Chromosome Location	chr2:37099339-37099340
allele	A/G
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	SPI1	chr2:37099172-37099522	HL-60	blood:	n/a	n/a
2	RAD21	chr2:37099310-37099519	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr2:37099302-37099590	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr2:37099186-37099521	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr2:37099336-37099459	K562	blood:	n/a	n/a
6	CTCF	chr2:37099288-37099533	K562	blood:	n/a	n/a
7	RAD21	chr2:37099318-37099546	SK-N-SH_RA	brain:	n/a	n/a
8	RAD21	chr2:37099314-37099502	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RNU6-577P	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10176270	0.80[CHD][hapmap]
rs10193295	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap]
rs10490657	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11124555	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap]
rs12476515	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13418962	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17020071	1.00[JPT][hapmap]
rs17443495	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs17496249	0.81[EUR][1000 genomes]
rs2003585	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2110942	0.85[EUR][1000 genomes]
rs2110944	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245109	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2540926	0.90[ASN][1000 genomes]
rs2540998	0.84[CHB][hapmap]
rs2691106	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2691112	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2717493	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28527412	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770774	0.92[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs3770781	0.82[CEU][hapmap]
rs3845778	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3845780	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs4016033	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4389320	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4670638	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs57747847	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6752845	0.89[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs7561572	0.81[ASN][1000 genomes]
rs7573966	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7588378	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs888083	0.81[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004483	chr2:36875235-37356812	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv535644	chr2:36875235-37356812	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv428395	chr2:36990348-37300352	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2252032	EIF2AK2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37065800-37104200	Weak transcription	Right Ventricle	heart
2	chr2:37067400-37103200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:37067600-37103000	Weak transcription	Small Intestine	intestine
4	chr2:37067600-37146200	Weak transcription	Psoas Muscle	Psoas
5	chr2:37075600-37101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:37075600-37139200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:37075800-37106600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:37076800-37111600	Weak transcription	Brain Germinal Matrix	brain
9	chr2:37077000-37102400	Weak transcription	Brain Angular Gyrus	brain
10	chr2:37077000-37102400	Weak transcription	Gastric	stomach
11	chr2:37077000-37116200	Weak transcription	Hela-S3	cervix
12	chr2:37077000-37116200	Weak transcription	NHLF	lung
13	chr2:37077200-37102400	Weak transcription	Aorta	Aorta
14	chr2:37077200-37102400	Weak transcription	Pancreas	Pancrea
15	chr2:37077200-37144400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:37077400-37136600	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:37078200-37118400	Weak transcription	Fetal Brain Male	brain
18	chr2:37079200-37111000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:37080600-37105800	Strong transcription	Primary B cells from cord blood	blood
20	chr2:37081600-37100200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:37082200-37115600	Weak transcription	Stomach Mucosa	stomach
22	chr2:37083800-37108000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:37084200-37103200	Weak transcription	HSMMtube	muscle
24	chr2:37084400-37102400	Weak transcription	Spleen	Spleen
25	chr2:37085800-37102000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:37086200-37100400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:37086400-37099400	Weak transcription	Ovary	ovary
28	chr2:37086400-37099400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:37086400-37103600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:37087400-37146200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:37088000-37101200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:37088000-37101400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:37089000-37101400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:37090600-37105600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:37090800-37105200	Strong transcription	Adipose Nuclei	Adipose
36	chr2:37090800-37114200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:37091000-37105800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:37091000-37114000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:37091200-37101200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:37091200-37114400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:37091400-37105800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:37091600-37100800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:37091600-37101400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:37092800-37115600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:37093200-37099600	Strong transcription	Dnd41	blood
46	chr2:37093200-37101600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:37093200-37105800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr2:37093400-37100400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:37093600-37102400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:37093600-37102400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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