Variant report

Variant	rs6731176
Chromosome Location	chr2:128071003-128071004
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	SPI1	chr2:128070966-128071274	HL-60	blood:	n/a	chr2:128071118-128071127 chr2:128071115-128071128 chr2:128071122-128071131 chr2:128071116-128071129
2	EP300	chr2:128070888-128071465	GM12878	blood:	n/a	chr2:128071117-128071131
3	BCL11A	chr2:128070897-128071285	GM12878	blood:	n/a	chr2:128071122-128071131
4	POU2F2	chr2:128070918-128071293	GM12878	blood:	n/a	chr2:128071185-128071192 chr2:128071183-128071193 chr2:128071179-128071197 chr2:128071177-128071198 chr2:128071177-128071199 chr2:128071181-128071196 chr2:128071184-128071193
5	TBL1XR1	chr2:128070944-128071357	GM12878	blood:	n/a	n/a
6	RCOR1	chr2:128070938-128071287	GM12878	blood:	n/a	n/a
7	EBF1	chr2:128070859-128071221	GM12878	blood:	n/a	n/a
8	EBF1	chr2:128070929-128071256	GM12878	blood:	n/a	n/a
9	RUNX3	chr2:128070868-128071321	GM12878	blood:	n/a	n/a
10	NFIC	chr2:128070910-128071315	GM12878	blood:	n/a	n/a
11	PML	chr2:128070986-128071241	GM12878	blood:	n/a	n/a
12	ATF2	chr2:128070887-128071411	GM12878	blood:	n/a	n/a
13	SPI1	chr2:128070558-128072295	GM12878	blood:	n/a	chr2:128071118-128071127 chr2:128071115-128071128 chr2:128071122-128071131 chr2:128071116-128071129
14	EP300	chr2:128070935-128071455	GM12878	blood:	n/a	chr2:128071117-128071131
15	EP300	chr2:128070947-128071353	GM12878	blood:	n/a	chr2:128071117-128071131
16	SPI1	chr2:128070917-128071364	GM12891	blood:	n/a	chr2:128071118-128071127 chr2:128071115-128071128 chr2:128071122-128071131 chr2:128071116-128071129
17	BCL11A	chr2:128070938-128071314	GM12878	blood:	n/a	chr2:128071122-128071131
18	REST	chr2:128070975-128071250	Hela-S3	cervix:	n/a	n/a
19	IRF4	chr2:128070920-128071415	GM12878	blood:	n/a	n/a
20	SPI1	chr2:128070945-128071254	GM12878	blood:	n/a	chr2:128071118-128071127 chr2:128071115-128071128 chr2:128071122-128071131 chr2:128071116-128071129
21	BHLHE40	chr2:128070917-128071466	GM12878	blood:	n/a	n/a
22	STAT3	chr2:128070969-128071407	MCF10A-Er-Src	breast:	n/a	chr2:128071122-128071133
23	BATF	chr2:128070987-128071264	GM12878	blood:	n/a	n/a
24	POU2F2	chr2:128070961-128071445	GM12891	blood:	n/a	chr2:128071185-128071192 chr2:128071183-128071193 chr2:128071179-128071197 chr2:128071177-128071198 chr2:128071177-128071199 chr2:128071181-128071196 chr2:128071184-128071193
25	SPI1	chr2:128070892-128071335	GM12878	blood:	n/a	chr2:128071118-128071127 chr2:128071115-128071128 chr2:128071122-128071131 chr2:128071116-128071129
26	CHD2	chr2:128070890-128071450	GM12878	blood:	n/a	n/a
27	SPI1	chr2:128070786-128071351	GM12891	blood:	n/a	chr2:128071118-128071127 chr2:128071115-128071128 chr2:128071122-128071131 chr2:128071116-128071129
28	POU2F2	chr2:128070873-128071455	GM12878	blood:	n/a	chr2:128071185-128071192 chr2:128071183-128071193 chr2:128071179-128071197 chr2:128071177-128071198 chr2:128071177-128071199 chr2:128071181-128071196 chr2:128071184-128071193
29	BCLAF1	chr2:128070836-128071267	GM12878	blood:	n/a	chr2:128071122-128071131
30	RUNX3	chr2:128070864-128071314	GM12878	blood:	n/a	n/a
31	IRF4	chr2:128070883-128071384	GM12878	blood:	n/a	n/a
32	ATF2	chr2:128070894-128071344	GM12878	blood:	n/a	n/a
33	BATF	chr2:128070967-128071251	GM12878	blood:	n/a	n/a
34	STAT3	chr2:128070927-128071414	MCF10A-Er-Src	breast:	n/a	chr2:128071122-128071133

Variant related genes	Relation type
RNU6-1147P	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10209678	0.86[ASN][1000 genomes]
rs10803585	0.95[ASN][1000 genomes]
rs10928761	0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs11886231	0.92[ASN][1000 genomes]
rs11890187	1.00[ASN][1000 genomes]
rs11901355	0.87[ASN][1000 genomes]
rs12052483	0.94[ASN][1000 genomes]
rs12463451	0.97[ASN][1000 genomes]
rs12463909	0.81[EUR][1000 genomes]
rs12465955	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12477214	0.93[ASN][1000 genomes]
rs12479003	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12622436	0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12623948	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12692064	0.86[ASN][1000 genomes]
rs12989081	0.93[ASN][1000 genomes]
rs12989154	0.96[ASN][1000 genomes]
rs12991062	0.87[ASN][1000 genomes]
rs12991768	0.91[ASN][1000 genomes]
rs13029237	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1566822	0.83[EUR][1000 genomes]
rs1566823	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs17015199	1.00[ASN][1000 genomes]
rs1799808	0.82[MEX][hapmap]
rs1850689	0.93[ASN][1000 genomes]
rs2090574	0.95[ASN][1000 genomes]
rs2174270	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276583	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2896980	0.94[ASN][1000 genomes]
rs3088374	0.95[MEX][hapmap]
rs34832797	0.96[ASN][1000 genomes]
rs35293119	0.94[ASN][1000 genomes]
rs35328149	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3768866	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3902960	0.83[EUR][1000 genomes]
rs4150407	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4150441	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4150454	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4150477	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]
rs4150495	0.92[ASN][1000 genomes]
rs4150496	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]
rs4233583	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4233584	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4497825	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4560059	0.81[EUR][1000 genomes]
rs4662575	0.91[ASN][1000 genomes]
rs4662578	1.00[ASN][1000 genomes]
rs4662580	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.99[ASN][1000 genomes]
rs4662710	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4662711	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4662717	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4662722	0.99[ASN][1000 genomes]
rs4662725	0.94[ASN][1000 genomes]
rs55905117	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55998967	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58475809	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59566504	0.96[ASN][1000 genomes]
rs62157549	1.00[ASN][1000 genomes]
rs62157555	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62160261	0.86[ASN][1000 genomes]
rs6430935	0.88[ASN][1000 genomes]
rs6712213	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6712446	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6712551	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6732279	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6761391	0.89[CEU][hapmap]
rs6761447	1.00[ASN][1000 genomes]
rs71414745	0.81[ASN][1000 genomes]
rs7568261	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7580658	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs7589451	0.95[ASN][1000 genomes]
rs867304	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9636235	0.82[EUR][1000 genomes]
rs9636236	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs9636237	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs9789510	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6731176	ERCC3	cis	cerebellum	SCAN
rs6731176	MAP3K2	cis	lymphoblastoid	seeQTL
rs6731176	ERCC3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128052400-128071200	Weak transcription	Fetal Brain Male	brain
2	chr2:128052800-128071800	Weak transcription	NHLF	lung
3	chr2:128053000-128071600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:128058600-128085600	Strong transcription	Primary B cells from cord blood	blood
5	chr2:128059400-128082800	Strong transcription	Liver	Liver
6	chr2:128059400-128109600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:128059800-128093000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:128061200-128077600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:128061600-128098200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:128061800-128096800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:128062000-128077600	Strong transcription	Fetal Intestine Large	intestine
12	chr2:128062000-128077800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:128062000-128083200	Strong transcription	Primary T cells from cord blood	blood
14	chr2:128062000-128085000	Strong transcription	Duodenum Mucosa	Duodenum
15	chr2:128062000-128086600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:128062400-128094000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr2:128062600-128071800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:128062600-128077600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:128062600-128077800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:128062600-128077800	Strong transcription	Dnd41	blood
21	chr2:128062600-128078000	Strong transcription	Fetal Thymus	thymus
22	chr2:128062600-128083400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr2:128062600-128083400	Strong transcription	Thymus	Thymus
24	chr2:128062600-128089400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:128062800-128077800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr2:128062800-128098000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:128063000-128076200	Strong transcription	Brain Anterior Caudate	brain
28	chr2:128063000-128076800	Strong transcription	Osteobl	bone
29	chr2:128063000-128077400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:128063000-128078400	Strong transcription	Adipose Nuclei	Adipose
31	chr2:128063000-128080200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:128063000-128089200	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:128063200-128076600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:128063200-128080200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:128063400-128077800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:128063400-128077800	Strong transcription	Fetal Lung	lung
37	chr2:128063400-128084800	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:128063400-128098400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:128063600-128078000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:128063600-128081200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:128063600-128083400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr2:128063600-128091800	Strong transcription	Placenta	Placenta
43	chr2:128063800-128072400	Strong transcription	Brain Substantia Nigra	brain
44	chr2:128063800-128075400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr2:128063800-128077200	Strong transcription	A549	lung
46	chr2:128063800-128077800	Strong transcription	Fetal Muscle Leg	muscle
47	chr2:128063800-128081400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:128063800-128083400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:128064200-128083800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:128064200-128090000	Weak transcription	Psoas Muscle	Psoas

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