Variant report

Variant	rs2276683
Chromosome Location	chr2:128146762-128146763
allele	C/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	CHD1	chr2:128143649-128147067	IMR90	lung:	n/a	chr2:128145167-128145177
2	EBF1	chr2:128144520-128147130	GM12878	blood:	n/a	chr2:128145148-128145157 chr2:128145148-128145157 chr2:128147052-128147061
3	CEBPB	chr2:128146481-128146783	Hela-S3	cervix:	n/a	n/a
4	MYC	chr2:128144656-128146796	A549	lung:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
5	CUX1	chr2:128146736-128146874	K562	blood:	n/a	n/a
6	POLR2A	chr2:128144487-128146762	GM12891	blood:	n/a	n/a
7	RAD21	chr2:128145840-128146787	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr2:128146515-128146765	HepG2	liver:	n/a	n/a
9	E2F4	chr2:128146695-128146858	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:128143986..128147167-chr2:128178825..128181533,4	MCF-7	breast:
2	chr2:128050445..128053038-chr2:128144842..128147674,3	K562	blood:
3	chr2:128145128..128146772-chr2:128281228..128284838,3	MCF-7	breast:
4	chr2:128143841..128146885-chr2:128179410..128184717,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PROC-1	chr2:128146687-128146924	NONHSAT074148
2	lnc-PROC-1	chr2:128146687-128146958	NONHSAT074150
3	lnc-PROC-1	chr2:128146687-128146953	NONHSAT074153

Variant related genes	Relation type
MAP3K2	TF binding region
ENSG00000163161	Chromatin interaction
ENSG00000163166	Chromatin interaction
ENSG00000264075	Chromatin interaction
ENSG00000115718	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10167294	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10928764	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1143407	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11684068	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11899601	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12613252	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12613254	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12613413	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12614320	0.86[EUR][1000 genomes]
rs12617858	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12619391	0.86[EUR][1000 genomes]
rs13017103	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13034157	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13390029	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13403918	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13409933	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13414676	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13429925	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2134794	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2139142	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28807127	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3088374	0.82[ASN][1000 genomes]
rs34006114	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34601617	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35708549	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738948	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3893313	0.81[EUR][1000 genomes]
rs4150434	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4150492	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4150506	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4150514	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4300780	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4359587	0.81[EUR][1000 genomes]
rs4662721	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4662724	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58063879	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59027829	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6430937	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6716392	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6735779	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6761391	0.88[ASN][1000 genomes]
rs67771362	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9923	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327412	chr2:128144082-128146880	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2276683	AC068282.3	cis	Whole Blood	GTEx
rs2276683	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2276683	AC068282.3	cis	Heart Left Ventricle	GTEx
rs2276683	MAP3K2	cis	multi-tissue	Pritchard
rs2276683	AC068282.3	cis	Stomach	GTEx
rs2276683	AC068282.3	cis	Artery Tibial	GTEx
rs2276683	AC068282.3	cis	Nerve Tibial	GTEx
rs2276683	AC068282.3	cis	Thyroid	GTEx
rs2276683	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs2276683	AC068282.3	cis	lung	GTEx
rs2276683	AC068282.3	cis	Esophagus Muscularis	GTEx
rs2276683	AC068282.3	cis	Esophagus Mucosa	GTEx
rs2276683	AC068282.3	cis	Artery Aorta	GTEx
rs2276683	AC068282.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128145800-128146800	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr2:128145800-128146800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:128145800-128146800	Flanking Active TSS	Hela-S3	cervix
4	chr2:128145800-128148400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr2:128146000-128146800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:128146000-128146800	Enhancers	Small Intestine	intestine
7	chr2:128146000-128146800	Flanking Active TSS	A549	lung
8	chr2:128146000-128158400	Weak transcription	Ovary	ovary
9	chr2:128146200-128147000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:128146200-128147600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:128146200-128148000	Enhancers	Primary T cells from cord blood	blood
12	chr2:128146200-128148000	Flanking Active TSS	GM12878-XiMat	blood
13	chr2:128146200-128148200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr2:128146200-128148800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:128146200-128150600	Enhancers	Fetal Thymus	thymus
16	chr2:128146400-128146800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:128146400-128146800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:128146400-128146800	Enhancers	Stomach Mucosa	stomach
19	chr2:128146400-128146800	Flanking Active TSS	HepG2	liver
20	chr2:128146400-128146800	Enhancers	HMEC	breast
21	chr2:128146400-128146800	Enhancers	HSMMtube	muscle
22	chr2:128146400-128147000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr2:128146400-128147200	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:128146400-128147400	Weak transcription	Fetal Brain Female	brain
25	chr2:128146400-128147600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr2:128146400-128147800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:128146400-128147800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:128146400-128147800	Enhancers	Fetal Intestine Small	intestine
29	chr2:128146400-128147800	Enhancers	Dnd41	blood
30	chr2:128146400-128148200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:128146400-128148400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:128146400-128148400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr2:128146400-128148400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr2:128146400-128148400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr2:128146400-128148600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:128146400-128148600	Enhancers	Thymus	Thymus
37	chr2:128146400-128149600	Weak transcription	NH-A	brain
38	chr2:128146400-128150400	Enhancers	Primary B cells from peripheral blood	blood
39	chr2:128146400-128150400	Weak transcription	Aorta	Aorta
40	chr2:128146400-128155200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:128146400-128165200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:128146600-128146800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr2:128146600-128146800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:128146600-128146800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:128146600-128146800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr2:128146600-128146800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
47	chr2:128146600-128146800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr2:128146600-128146800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr2:128146600-128146800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:128146600-128146800	Weak transcription	Lung	lung

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