Variant report

Variant	rs4684306
Chromosome Location	chr3:17016127-17016128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11128812	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11128813	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11128814	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11717433	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11717649	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11721224	0.84[AMR][1000 genomes]
rs11915356	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12108065	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12233492	0.81[JPT][hapmap]
rs12488103	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12491516	0.83[ASN][1000 genomes]
rs12492983	0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12494582	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12495362	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1372071	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17042909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17042920	0.95[ASN][1000 genomes]
rs1806555	0.81[JPT][hapmap]
rs2014490	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs34322012	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796299	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs3906814	0.84[JPT][hapmap]
rs4131153	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4289331	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4334629	0.87[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4383507	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4402923	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4416363	0.89[ASN][1000 genomes]
rs4452313	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4577450	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4684305	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4684307	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4684308	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4685405	0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4685410	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4685411	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4685416	0.84[ASN][1000 genomes]
rs4685419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4685423	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4685424	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes]
rs4685425	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs4685426	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs58679681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58750701	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58765457	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59737477	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62246033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62247183	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62247186	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62247188	0.82[AMR][1000 genomes]
rs62247190	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6796352	0.83[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6803135	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6806862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7612044	0.87[CHB][hapmap]
rs7617779	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7634374	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7639882	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7648912	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7653834	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs964576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9821630	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9824172	0.80[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9825009	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844888	0.86[JPT][hapmap]
rs9853476	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9879150	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs9883633	0.86[CHB][hapmap];0.85[JPT][hapmap]

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	nsv980048	chr3:16995372-17016178	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4684306	CHCHD4	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17009200-17026600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:17013400-17016200	Weak transcription	Adipose Nuclei	Adipose
3	chr3:17013800-17016200	Weak transcription	Fetal Heart	heart
4	chr3:17014600-17016600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:17014800-17019600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:17014800-17033600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:17014800-17038800	Weak transcription	Primary B cells from cord blood	blood
8	chr3:17015000-17017400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:17015000-17018000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:17015000-17019400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:17015400-17016200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:17015400-17016400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:17015400-17016800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr3:17015400-17017400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr3:17015400-17017600	Enhancers	Left Ventricle	heart
16	chr3:17015600-17016200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:17015600-17016400	Enhancers	Ovary	ovary
18	chr3:17015600-17016400	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr3:17015600-17017000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:17015600-17017400	Enhancers	Right Atrium	heart
21	chr3:17015600-17017600	Enhancers	Psoas Muscle	Psoas
22	chr3:17015600-17019000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:17015800-17016200	Weak transcription	Right Ventricle	heart
24	chr3:17015800-17016400	Weak transcription	Pancreas	Pancrea
25	chr3:17015800-17017800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:17016000-17016400	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:17016000-17016400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr3:17016000-17020000	Weak transcription	Aorta	Aorta
29	chr3:17016000-17020600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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