Variant report

Variant	rs9824172
Chromosome Location	chr3:16974123-16974124
allele	G/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	E2F4	chr3:16973973-16974152	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
MIR3714	TF binding region
PLCL2	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10865746	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs11128812	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11128813	0.87[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs1156336	0.82[ASN][1000 genomes]
rs11915356	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11926952	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11928330	0.82[ASN][1000 genomes]
rs11928414	0.82[ASN][1000 genomes]
rs12108065	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs12233492	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs12487288	0.85[JPT][hapmap]
rs12488103	0.87[ASN][1000 genomes]
rs12492983	0.83[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12494582	0.82[ASN][1000 genomes]
rs12497667	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs13058764	0.84[JPT][hapmap]
rs13080108	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs1372071	0.83[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1372072	0.82[ASN][1000 genomes]
rs1441035	0.86[JPT][hapmap]
rs17042909	0.80[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs17042920	0.90[ASN][1000 genomes]
rs17272796	0.86[JPT][hapmap]
rs1806556	0.84[JPT][hapmap]
rs2014490	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs2881771	0.83[ASN][1000 genomes]
rs34322012	0.80[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs3796299	0.80[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs3924971	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4131153	0.80[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4289331	0.80[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4334629	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs4353792	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4383507	0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4402923	0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4452313	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4461404	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4472039	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4535211	0.86[JPT][hapmap]
rs4577450	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs4602367	0.86[JPT][hapmap]
rs4684305	0.80[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4684306	0.80[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4684307	0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs4684308	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4685403	0.82[ASN][1000 genomes]
rs4685404	0.86[JPT][hapmap]
rs4685405	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4685409	0.86[JPT][hapmap]
rs4685411	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs4685416	0.83[EUR][1000 genomes]
rs4685418	0.81[JPT][hapmap]
rs4685423	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4685424	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4685425	0.80[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4685426	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs58750701	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58765457	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6442660	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6762816	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6780191	0.86[JPT][hapmap]
rs6796352	0.80[JPT][hapmap]
rs6809087	0.86[JPT][hapmap]
rs7610811	0.83[CHB][hapmap]
rs7611127	0.86[JPT][hapmap]
rs7612044	0.85[JPT][hapmap]
rs7617672	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7617779	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7639882	0.83[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7648912	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs7653027	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7653834	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs964576	0.86[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9810017	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9821630	0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9825009	0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9830460	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs9841259	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs9853476	0.83[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9854760	0.89[JPT][hapmap]
rs9862613	0.84[JPT][hapmap]
rs9872237	0.82[ASN][1000 genomes]
rs9879150	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9880307	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs9881521	0.81[JPT][hapmap]
rs9883633	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9824172	CHCHD4	cis	parietal	SCAN

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

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	chr3:16970200-16974200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:16970200-16974600	Weak transcription	Gastric	stomach
12	chr3:16970200-16975600	Weak transcription	Pancreas	Pancrea
13	chr3:16970400-16977400	Weak transcription	Thymus	Thymus
14	chr3:16970800-16977000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:16971400-16974200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:16971400-16975600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:16971600-16974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:16971600-16974600	Weak transcription	Left Ventricle	heart
19	chr3:16971600-16975600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:16971600-16975600	Weak transcription	Adipose Nuclei	Adipose
21	chr3:16971600-16975600	Weak transcription	Spleen	Spleen
22	chr3:16971600-16982400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:16971800-16974200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:16972000-16977600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:16972200-16974600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:16972200-16977200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:16972400-16974600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:16972400-16975600	Weak transcription	Psoas Muscle	Psoas
29	chr3:16972400-16983600	Weak transcription	Brain Angular Gyrus	brain
30	chr3:16972600-16974200	Weak transcription	Primary T cells from cord blood	blood
31	chr3:16972600-16974200	Weak transcription	Ovary	ovary
32	chr3:16972600-16974200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:16972600-16974400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:16972600-16975600	Weak transcription	Right Ventricle	heart
35	chr3:16972600-16975800	Weak transcription	Right Atrium	heart
36	chr3:16973000-16976400	Strong transcription	Primary B cells from cord blood	blood
37	chr3:16973200-16974600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:16973400-16980400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr3:16973600-16974200	Weak transcription	Fetal Heart	heart
40	chr3:16973600-16977000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:16973800-16974600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:16973800-16975600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:16973800-16985000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr3:16974000-16974800	Enhancers	Primary B cells from peripheral blood	blood
45	chr3:16974000-16974800	Enhancers	Stomach Mucosa	stomach
46	chr3:16974000-16974800	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr3:16974000-16975000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:16974000-16975200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:16974000-16975200	Flanking Active TSS	GM12878-XiMat	blood
50	chr3:16974000-16978200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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