Variant report

Variant	rs10067046
Chromosome Location	chr5:112676024-112676025
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10036581	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10057210	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10072511	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10076501	0.85[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1038918	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10519341	1.00[YRI][hapmap]
rs10900684	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11241200	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11748642	0.84[ASN][1000 genomes]
rs11948072	0.83[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13153071	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13190054	0.81[CEU][hapmap]
rs1517206	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1517208	0.87[AMR][1000 genomes]
rs1517210	0.84[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes]
rs154039	0.82[AMR][1000 genomes]
rs154040	0.86[AMR][1000 genomes]
rs164251	0.82[JPT][hapmap]
rs17135473	1.00[YRI][hapmap]
rs173903	0.84[AMR][1000 genomes]
rs1822487	1.00[YRI][hapmap]
rs1838205	0.81[CHB][hapmap];0.80[MEX][hapmap]
rs1838207	0.85[CEU][hapmap]
rs1845290	0.84[CEU][hapmap];0.90[AMR][1000 genomes]
rs1850408	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2165928	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2416310	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs255856	0.84[CEU][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes]
rs255858	0.87[AMR][1000 genomes]
rs255863	0.85[AMR][1000 genomes]
rs255867	0.86[AMR][1000 genomes]
rs255874	0.86[AMR][1000 genomes]
rs26960	0.87[AMR][1000 genomes]
rs27566	0.84[CEU][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes]
rs36612	0.81[AMR][1000 genomes]
rs3857435	0.84[CEU][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes]
rs4108702	0.81[CHD][hapmap];0.96[MEX][hapmap]
rs423089	0.82[JPT][hapmap]
rs459428	0.82[JPT][hapmap]
rs461034	0.93[JPT][hapmap]
rs463216	0.87[JPT][hapmap]
rs465898	0.87[JPT][hapmap]
rs4705812	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4705813	0.89[AMR][1000 genomes]
rs485210	0.88[MEX][hapmap]
rs492346	0.88[MEX][hapmap]
rs6594700	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6594711	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs6869097	0.96[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6871668	1.00[YRI][hapmap]
rs6873400	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6873755	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs6875238	0.89[AMR][1000 genomes]
rs6879612	0.82[AMR][1000 genomes]
rs6894434	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7702120	0.84[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes]
rs7722276	0.85[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap]
rs7735247	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs971372	0.81[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10067046	YTHDC2	cis	cerebellum	SCAN
rs10067046	YTHDC2	cis	parietal	SCAN
rs10067046	LILRP2	trans	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112666800-112678600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:112667000-112681000	Weak transcription	Esophagus	oesophagus
3	chr5:112667200-112678800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:112667200-112678800	Weak transcription	HMEC	breast
5	chr5:112667200-112680400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:112667200-112680600	Weak transcription	NHEK	skin
7	chr5:112667200-112680800	Weak transcription	Right Ventricle	heart
8	chr5:112667200-112681000	Weak transcription	Pancreas	Pancrea
9	chr5:112667200-112693400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:112671400-112676400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:112673000-112676400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:112673200-112676800	Weak transcription	Fetal Stomach	stomach
13	chr5:112673200-112678400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:112674200-112676200	Weak transcription	Left Ventricle	heart
15	chr5:112674400-112676200	Weak transcription	Right Atrium	heart
16	chr5:112674600-112678800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:112675800-112677000	Enhancers	HUVEC	blood vessel
18	chr5:112675800-112679000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:112676000-112676200	Active TSS	Aorta	Aorta
20	chr5:112676000-112676400	Flanking Active TSS	Fetal Heart	heart

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