Variant report

Variant	rs1965429
Chromosome Location	chr5:112679373-112679374
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10035686	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10041899	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10042223	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10051834	0.88[CEU][hapmap];0.81[YRI][hapmap]
rs10053654	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10062004	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10074214	0.89[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap]
rs1116547	0.82[YRI][hapmap]
rs1120091	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11241201	0.82[YRI][hapmap]
rs11241206	0.81[YRI][hapmap]
rs12523255	0.81[YRI][hapmap]
rs13157609	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13188946	0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13359330	0.82[EUR][1000 genomes]
rs1366393	0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1517207	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1607159	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17135608	0.80[YRI][hapmap]
rs1845291	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1850407	0.96[CEU][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1850410	0.81[YRI][hapmap]
rs1850412	0.89[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap]
rs2222144	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2248930	0.88[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs255861	0.83[EUR][1000 genomes]
rs255862	0.80[EUR][1000 genomes]
rs255865	0.82[EUR][1000 genomes]
rs255866	0.83[EUR][1000 genomes]
rs255877	0.82[EUR][1000 genomes]
rs26959	0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs26961	0.96[CEU][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs26964	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs26966	0.96[CEU][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs26967	0.83[EUR][1000 genomes]
rs26968	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs26969	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs27567	0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs348928	0.88[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs348929	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs348930	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs348931	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs348932	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs348947	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs348956	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs348961	0.88[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs348962	0.88[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs348963	0.88[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs364738	0.88[JPT][hapmap]
rs367943	0.88[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs4331889	0.96[CEU][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs444322	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs455435	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs460079	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs463167	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs463249	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs4705814	0.80[YRI][hapmap]
rs644154	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs6594701	0.96[CEU][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6594704	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs6594705	0.89[CEU][hapmap];0.82[YRI][hapmap]
rs6594707	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6594710	0.96[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs6594712	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6860495	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6861668	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6864528	0.82[YRI][hapmap]
rs6867397	0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6871812	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6880749	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6894687	0.83[MEX][hapmap]
rs6896650	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7708084	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7714734	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7717422	0.89[CEU][hapmap]
rs7725589	0.89[CEU][hapmap];0.84[YRI][hapmap]
rs7731465	0.96[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7731854	0.81[EUR][1000 genomes]
rs7734061	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7734304	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9326884	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9326886	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9326887	0.96[CEU][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9326888	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9326889	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9632462	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1965429	YTHDC2	cis	cerebellum	SCAN
rs1965429	NCRNA00219	cis	cerebellum	SCAN
rs1965429	MCC	cis	cerebellum	SCAN
rs1965429	YTHDC2	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112667000-112681000	Weak transcription	Esophagus	oesophagus
2	chr5:112667200-112680400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:112667200-112680600	Weak transcription	NHEK	skin
4	chr5:112667200-112680800	Weak transcription	Right Ventricle	heart
5	chr5:112667200-112681000	Weak transcription	Pancreas	Pancrea
6	chr5:112667200-112693400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:112676600-112679800	Weak transcription	Left Ventricle	heart
8	chr5:112678400-112679400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:112678400-112679800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:112678600-112679400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:112678800-112679400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:112678800-112679600	Flanking Active TSS	Fetal Heart	heart
13	chr5:112678800-112681400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:112678800-112681600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:112678800-112682400	Enhancers	HMEC	breast
16	chr5:112679000-112679400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:112679000-112679400	Enhancers	Right Atrium	heart
18	chr5:112679000-112682000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:112679200-112679800	Enhancers	Fetal Stomach	stomach

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