Variant report

Variant	rs2276682
Chromosome Location	chr2:128146462-128146463
allele	A/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	RUNX3	chr2:128144347-128146478	GM12878	blood:	n/a	n/a
2	RELA	chr2:128145433-128146520	GM10847	blood:	n/a	n/a
3	MAX	chr2:128145370-128146614	A549	lung:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
4	CHD1	chr2:128143649-128147067	IMR90	lung:	n/a	chr2:128145167-128145177
5	POLR2A	chr2:128145699-128146462	GM12891	blood:	n/a	n/a
6	KAP1	chr2:128145883-128146549	HEK293	kidney:	n/a	n/a
7	ATF2	chr2:128145303-128146473	GM12878	blood:	n/a	chr2:128145544-128145558 chr2:128145565-128145579
8	EP300	chr2:128144748-128146508	GM12878	blood:	n/a	chr2:128145703-128145719 chr2:128145712-128145728 chr2:128145498-128145507 chr2:128145501-128145517 chr2:128145468-128145484
9	RELA	chr2:128145378-128146483	GM19099	blood:	n/a	n/a
10	WRNIP1	chr2:128145782-128146599	GM12878	blood:	n/a	n/a
11	MBD4	chr2:128145684-128146544	HepG2	liver:	n/a	n/a
12	CHD1	chr2:128144476-128146698	GM12878	blood:	n/a	chr2:128145167-128145177
13	EBF1	chr2:128144520-128147130	GM12878	blood:	n/a	chr2:128145148-128145157 chr2:128145148-128145157 chr2:128147052-128147061
14	POLR2A	chr2:128144374-128146684	HepG2	liver:	n/a	n/a
15	JUND	chr2:128144568-128146498	K562	blood:	n/a	n/a
16	POLR2A	chr2:128145694-128146476	GM12891	blood:	n/a	n/a
17	CHD2	chr2:128144621-128146564	GM12878	blood:	n/a	chr2:128145167-128145177
18	CHD2	chr2:128146268-128146468	K562	blood:	n/a	n/a
19	MXI1	chr2:128144583-128146464	GM12878	blood:	n/a	chr2:128145893-128145902
20	RELA	chr2:128144484-128146510	GM18951	blood:	n/a	n/a
21	MTA3	chr2:128144424-128146757	GM12878	blood:	n/a	n/a
22	KAP1	chr2:128145845-128146625	U2OS	brain:	n/a	n/a
23	MYC	chr2:128144656-128146796	A549	lung:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
24	POLR2A	chr2:128144416-128146634	GM12891	blood:	n/a	n/a
25	MAX	chr2:128144555-128146486	A549	lung:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
26	POLR2A	chr2:128144400-128146508	GM12878	blood:	n/a	n/a
27	RELA	chr2:128144472-128146616	GM12891	blood:	n/a	n/a
28	IKZF1	chr2:128145916-128146609	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:128144362-128146584	GM12878	blood:	n/a	n/a
30	POLR2A	chr2:128144583-128146572	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:128144487-128146762	GM12891	blood:	n/a	n/a
32	MXI1	chr2:128142981-128146528	SK-N-SH	brain:	n/a	chr2:128145893-128145902
33	POLR2A	chr2:128143894-128146570	MCF10A-Er-Src	breast:	n/a	n/a
34	RAD21	chr2:128145840-128146787	Hela-S3	cervix:	n/a	n/a
35	MTA3	chr2:128146025-128146692	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:128144344-128146603	GM12892	blood:	n/a	n/a
37	POLR2A	chr2:128145656-128146567	GM12892	blood:	n/a	n/a
38	POLR2A	chr2:128144397-128146539	HepG2	liver:	n/a	n/a
39	POLR2A	chr2:128144869-128146647	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr2:128143818-128146726	IMR90	lung:	n/a	n/a
41	EP300	chr2:128144623-128146667	GM12878	blood:	n/a	chr2:128145703-128145719 chr2:128145712-128145728 chr2:128145498-128145507 chr2:128145501-128145517 chr2:128145468-128145484
42	MAX	chr2:128144371-128146646	HepG2	liver:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
43	MAX	chr2:128144395-128146618	A549	lung:	n/a	chr2:128145890-128145905 chr2:128145892-128145902
44	RUNX3	chr2:128144710-128146462	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:128144417-128146625	PBDE	blood:	n/a	n/a
46	POLR2A	chr2:128144531-128146636	GM12878	blood:	n/a	n/a
47	POLR2A	chr2:128144503-128146566	GM12878	blood:	n/a	n/a
48	TBL1XR1	chr2:128144473-128146551	GM12878	blood:	n/a	n/a
49	POU2F2	chr2:128144621-128146474	GM12878	blood:	n/a	chr2:128146295-128146305 chr2:128146292-128146307 chr2:128146295-128146304 chr2:128146296-128146303 chr2:128146294-128146306 chr2:128146294-128146304 chr2:128146293-128146304 chr2:128146293-128146304 chr2:128146288-128146310 chr2:128146295-128146305

No.	Distal block	Cell Line	Cell type
1	chr2:128143986..128147167-chr2:128178825..128181533,4	MCF-7	breast:
2	chr2:128100404..128103030-chr2:128144500..128146639,3	MCF-7	breast:
3	chr2:128143823..128146469-chr2:128456940..128459025,2	MCF-7	breast:
4	chr2:128050445..128053038-chr2:128144842..128147674,3	K562	blood:
5	chr2:128145128..128146772-chr2:128281228..128284838,3	MCF-7	breast:
6	chr2:128143841..128146885-chr2:128179410..128184717,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PROC-1	chr2:128145948-128146574	NONHSAT074151
2	lnc-PROC-1	chr2:128146457-128146574	NONHSAT074148
3	lnc-PROC-1	chr2:128146457-128146576	NONHSAT074150
4	lnc-PROC-1	chr2:128146190-128146574	NONHSAT074153
5	lnc-PROC-1	chr2:128146043-128146574	NONHSAT074152
6	lnc-PROC-1	chr2:128146457-128146574	NONHSAT074149

Variant related genes	Relation type
MAP3K2	TF binding region
ENSG00000236682	TF binding region
ENSG00000173349	Chromatin interaction
ENSG00000163166	Chromatin interaction
ENSG00000169967	Chromatin interaction
ENSG00000115718	Chromatin interaction
ENSG00000163161	Chromatin interaction
ENSG00000264075	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10167294	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10928764	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1143407	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11684068	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12614320	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12617858	0.86[EUR][1000 genomes];0.84[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];0.94[ASN][1000 genomes]
rs13390029	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13403918	0.86[EUR][1000 genomes];0.84[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	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2134794	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2139142	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276683	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	0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs34006114	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34601617	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34703177	0.95[CEU][hapmap]
rs35708549	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738948	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3893313	0.81[EUR][1000 genomes]
rs4150434	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4150492	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4150506	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4150514	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4300780	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4359587	0.81[EUR][1000 genomes]
rs4662721	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4662724	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58063879	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59027829	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6430937	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6716392	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6735779	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6747862	0.95[CEU][hapmap]
rs6761391	0.85[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs67771362	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7584659	0.80[ASN][1000 genomes]
rs9923	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2276682	AC068282.3	cis	Esophagus Mucosa	GTEx
rs2276682	AC068282.3	cis	Heart Left Ventricle	GTEx
rs2276682	AC068282.3	cis	Stomach	GTEx
rs2276682	MAP3K2	cis	multi-tissue	Pritchard
rs2276682	MAP3K2	cis	Cerebellum	GTEx
rs2276682	AC068282.3	cis	Artery Aorta	GTEx
rs2276682	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2276682	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs2276682	AC068282.3	cis	Muscle Skeletal	GTEx
rs2276682	AC068282.3	cis	Whole Blood	GTEx
rs2276682	MAP3K2	cis	Brain Pons	GTEx
rs2276682	AC068282.3	cis	Esophagus Muscularis	GTEx
rs2276682	MAP3K2	cis	Frontal Cortex	GTEx
rs2276682	AC068282.3	cis	Thyroid	GTEx
rs2276682	MAP3K2	cis	Temporal Cortex	GTEx
rs2276682	AC068282.3	cis	Artery Tibial	GTEx
rs2276682	AC068282.3	cis	Nerve Tibial	GTEx
rs2276682	AC068282.3	cis	lung	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128144200-128146600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:128144200-128146600	Active TSS	Colonic Mucosa	Colon
3	chr2:128145800-128146600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:128145800-128146600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:128145800-128146600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:128145800-128146600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:128145800-128146600	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr2:128145800-128146600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr2:128145800-128146600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr2:128145800-128146600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr2:128145800-128146600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:128145800-128146600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:128145800-128146600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr2:128145800-128146600	Flanking Active TSS	Fetal Intestine Large	intestine
15	chr2:128145800-128146600	Flanking Active TSS	Fetal Lung	lung
16	chr2:128145800-128146600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr2:128145800-128146600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr2:128145800-128146600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr2:128145800-128146600	Flanking Active TSS	Osteobl	bone
20	chr2:128145800-128146800	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr2:128145800-128146800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:128145800-128146800	Flanking Active TSS	Hela-S3	cervix
23	chr2:128145800-128148400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr2:128146000-128146600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:128146000-128146600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr2:128146000-128146600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:128146000-128146600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:128146000-128146600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:128146000-128146600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr2:128146000-128146600	Flanking Active TSS	Brain Anterior Caudate	brain
31	chr2:128146000-128146600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:128146000-128146600	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr2:128146000-128146600	Flanking Active TSS	Fetal Kidney	kidney
34	chr2:128146000-128146600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr2:128146000-128146600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr2:128146000-128146600	Enhancers	Spleen	Spleen
37	chr2:128146000-128146600	Flanking Active TSS	K562	blood
38	chr2:128146000-128146600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr2:128146000-128146800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:128146000-128146800	Enhancers	Small Intestine	intestine
41	chr2:128146000-128146800	Flanking Active TSS	A549	lung
42	chr2:128146000-128158400	Weak transcription	Ovary	ovary
43	chr2:128146200-128146600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:128146200-128146600	Enhancers	H9 Cell Line	embryonic stem cell
45	chr2:128146200-128146600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
46	chr2:128146200-128146600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
47	chr2:128146200-128146600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:128146200-128146600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr2:128146200-128146600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr2:128146200-128146600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links