Variant report

Variant	rs4150506
Chromosome Location	chr2:128020546-128020547
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	POLR2A	chr2:128020488-128020646	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128019410..128021681-chr2:128050187..128052921,2	MCF-7	breast:

Variant related genes	Relation type
ERCC3	TF binding region
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10167294	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10928764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1143407	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684068	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11899601	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12613252	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613254	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12614320	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12617858	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619391	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017103	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13034157	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13390029	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13403918	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409933	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13414676	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13429925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2134794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2139142	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276682	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2276683	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28807127	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3088374	0.91[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs34006114	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34441363	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34487399	0.92[EUR][1000 genomes]
rs34601617	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34703177	0.82[ASW][hapmap];0.95[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35708549	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3738948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893313	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4150434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150492	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150514	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300780	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4359587	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4528711	0.88[EUR][1000 genomes]
rs4662721	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4662724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58063879	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59027829	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6430937	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6716392	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6735779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6738811	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6747862	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6752139	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6761391	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs67771362	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7584659	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9752366	0.85[EUR][1000 genomes]
rs9923	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs4150506	MAP3K2	cis	Brain Pons	GTEx
rs4150506	AC068282.3	cis	Muscle Skeletal	GTEx
rs4150506	AC068282.3	cis	Thyroid	GTEx
rs4150506	MAP3K2	cis	lymphoblastoid	seeQTL
rs4150506	AC068282.3	cis	Whole Blood	GTEx
rs4150506	MAP3K2	cis	multi-tissue	Pritchard
rs4150506	TUBA3E	cis	parietal	SCAN
rs4150506	MAP3K2	cis	Frontal Cortex	GTEx
rs4150506	MAP3K2	cis	Temporal Cortex	GTEx
rs4150506	AC068282.3	cis	Esophagus Mucosa	GTEx
rs4150506	AC068282.3	cis	Nerve Tibial	GTEx
rs4150506	AC068282.3	cis	Artery Aorta	GTEx
rs4150506	AC068282.3	cis	Esophagus Muscularis	GTEx
rs4150506	AC068282.3	cis	lung	GTEx
rs4150506	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs4150506	MAP3K2	cis	Cerebellum	GTEx
rs4150506	MAP3K2	cis	cerebellum	SCAN
rs4150506	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4150506	GYPC	cis	parietal	SCAN
rs4150506	AC068282.3	cis	Stomach	GTEx
rs4150506	AC068282.3	cis	Heart Left Ventricle	GTEx
rs4150506	AC068282.3	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128012400-128028000	Weak transcription	Hela-S3	cervix
2	chr2:128012600-128026200	Weak transcription	Stomach Mucosa	stomach
3	chr2:128012800-128020800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:128013000-128020600	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:128013000-128020600	Strong transcription	Fetal Brain Female	brain
6	chr2:128013000-128020600	Strong transcription	Dnd41	blood
7	chr2:128013000-128020800	Strong transcription	Fetal Intestine Large	intestine
8	chr2:128013000-128021200	Strong transcription	Primary T cells from cord blood	blood
9	chr2:128013000-128021800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr2:128013200-128020600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:128013200-128020800	Strong transcription	Primary hematopoietic stem cells	blood
12	chr2:128013400-128020600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:128013400-128020600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:128013400-128020800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:128013400-128020800	Strong transcription	Left Ventricle	heart
16	chr2:128013400-128022400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:128013600-128020800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:128013600-128020800	Strong transcription	Liver	Liver
19	chr2:128013600-128036200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:128014000-128020600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:128014000-128020600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:128014000-128020600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:128014000-128020600	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:128014000-128020600	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr2:128014000-128020800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr2:128014000-128020800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:128014000-128020800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:128014000-128020800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr2:128014000-128021000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:128014000-128041000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:128014200-128020800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:128014200-128020800	Strong transcription	Primary B cells from cord blood	blood
33	chr2:128014200-128020800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:128014200-128021000	Strong transcription	Fetal Thymus	thymus
35	chr2:128014400-128020600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:128014400-128020600	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr2:128014400-128020800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:128014600-128041000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:128014800-128020600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:128016200-128027800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:128017200-128021400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:128017200-128027400	Weak transcription	Esophagus	oesophagus
43	chr2:128017400-128025000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:128017600-128026400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr2:128017600-128027800	Weak transcription	Small Intestine	intestine
46	chr2:128018200-128025600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:128018400-128024400	Weak transcription	HSMMtube	muscle
48	chr2:128018400-128024600	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:128018400-128024800	Weak transcription	NHDF-Ad	bronchial
50	chr2:128018800-128024200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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