Variant report

Variant	rs9880307
Chromosome Location	chr3:16974610-16974611
allele	A/C
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	ZNF143	chr3:16974584-16974781	GM12878	blood:	n/a	n/a
2	NFYB	chr3:16974468-16974866	GM12878	blood:	n/a	n/a
3	NFIC	chr3:16974353-16975158	GM12878	blood:	n/a	n/a
4	ZNF263	chr3:16974470-16974869	HEK293-T-REx	kidney:	n/a	n/a
5	RUNX3	chr3:16974440-16974799	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
MIR3714	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10865746	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11128815	0.83[ASN][1000 genomes]
rs11717329	0.86[ASN][1000 genomes]
rs11926952	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12233492	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12487288	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12492983	0.81[CHD][hapmap]
rs12497667	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12497953	0.83[ASN][1000 genomes]
rs13058764	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13059347	0.84[ASN][1000 genomes]
rs13071645	0.80[CEU][hapmap];0.85[ASN][1000 genomes]
rs13080108	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13317381	0.96[ASN][1000 genomes]
rs1348109	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1441035	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1441039	0.81[ASN][1000 genomes]
rs17272796	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1806555	0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1806556	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1837697	0.96[ASN][1000 genomes]
rs1837698	0.81[ASN][1000 genomes]
rs2014490	0.85[CHD][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs34149515	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35319117	0.82[ASN][1000 genomes]
rs3906814	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3924971	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4234539	0.81[ASN][1000 genomes]
rs4295151	0.81[ASN][1000 genomes]
rs4334629	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs4353792	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4423750	0.82[ASN][1000 genomes]
rs4461404	0.81[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4472039	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4535211	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4596131	0.81[ASN][1000 genomes]
rs4602367	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4618210	0.85[JPT][hapmap]
rs4684308	0.81[JPT][hapmap]
rs4685404	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4685405	0.86[JPT][hapmap]
rs4685408	0.97[ASN][1000 genomes]
rs4685409	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4685418	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4685420	0.82[ASN][1000 genomes]
rs4685421	0.83[ASN][1000 genomes]
rs4685426	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs4685427	0.85[JPT][hapmap]
rs55748719	0.83[ASN][1000 genomes]
rs6442660	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6762816	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6776032	0.81[ASN][1000 genomes]
rs6780191	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6781611	0.90[ASN][1000 genomes]
rs6783752	0.85[ASN][1000 genomes]
rs6797029	0.83[ASN][1000 genomes]
rs6805534	0.82[ASN][1000 genomes]
rs6807144	0.85[ASN][1000 genomes]
rs6809087	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7610811	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7611127	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7612044	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7617672	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7629171	0.88[ASN][1000 genomes]
rs7629676	0.85[ASN][1000 genomes]
rs7645335	0.81[CEU][hapmap];0.97[ASN][1000 genomes]
rs7653027	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9810017	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9824172	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs9830460	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9841259	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9844888	0.86[JPT][hapmap]
rs9854760	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9862613	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9879150	0.95[JPT][hapmap]
rs9881521	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9883633	0.81[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs9985404	0.83[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9880307	TMEM43	cis	cerebellum	SCAN
rs9880307	CHCHD4	cis	parietal	SCAN
rs9880307	C3orf20	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:16958000-16981800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:16959400-16986600	Weak transcription	Aorta	Aorta
3	chr3:16965000-16979000	Weak transcription	Lung	lung
4	chr3:16967000-16985000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:16967600-16977200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:16967800-16977800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:16969000-16977400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr3:16969600-16977400	Weak transcription	Fetal Thymus	thymus
9	chr3:16970000-16977000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:16970200-16975600	Weak transcription	Pancreas	Pancrea
11	chr3:16970400-16977400	Weak transcription	Thymus	Thymus
12	chr3:16970800-16977000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:16971400-16975600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:16971600-16975600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:16971600-16975600	Weak transcription	Adipose Nuclei	Adipose
16	chr3:16971600-16975600	Weak transcription	Spleen	Spleen
17	chr3:16971600-16982400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:16972000-16977600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:16972200-16977200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:16972400-16975600	Weak transcription	Psoas Muscle	Psoas
21	chr3:16972400-16983600	Weak transcription	Brain Angular Gyrus	brain
22	chr3:16972600-16975600	Weak transcription	Right Ventricle	heart
23	chr3:16972600-16975800	Weak transcription	Right Atrium	heart
24	chr3:16973000-16976400	Strong transcription	Primary B cells from cord blood	blood
25	chr3:16973400-16980400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:16973600-16977000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:16973800-16975600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:16973800-16985000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:16974000-16974800	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:16974000-16974800	Enhancers	Stomach Mucosa	stomach
31	chr3:16974000-16974800	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr3:16974000-16975000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:16974000-16975200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:16974000-16975200	Flanking Active TSS	GM12878-XiMat	blood
35	chr3:16974000-16978200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:16974200-16974800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr3:16974200-16975000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr3:16974200-16975000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:16974200-16975000	Enhancers	Ovary	ovary
40	chr3:16974200-16977200	Weak transcription	Dnd41	blood
41	chr3:16974200-16982600	Enhancers	Fetal Heart	heart
42	chr3:16974400-16974800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr3:16974400-16975600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:16974600-16974800	Genic enhancers	Primary T cells from cord blood	blood
45	chr3:16974600-16974800	Enhancers	Primary hematopoietic stem cells	blood
46	chr3:16974600-16974800	Enhancers	Gastric	stomach
47	chr3:16974600-16974800	Enhancers	Left Ventricle	heart
48	chr3:16974600-16975200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:16974600-16975200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr3:16974600-16975600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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