Variant report

Variant	rs4705812
Chromosome Location	chr5:112674497-112674498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112672794..112674511-chr5:112933592..112935108,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10036581	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10057210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067046	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]
rs10072511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10076501	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1038918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10900684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11241200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11748642	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11948072	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13153071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13190054	0.81[CEU][hapmap]
rs1517206	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1517210	0.84[CEU][hapmap]
rs1838205	0.84[MEX][hapmap]
rs1838207	0.85[CEU][hapmap]
rs1845290	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs1850408	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165928	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2416310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs255856	0.84[CEU][hapmap]
rs27566	0.84[CEU][hapmap]
rs3857435	0.84[CEU][hapmap]
rs4108702	0.92[MEX][hapmap]
rs461034	0.86[JPT][hapmap]
rs463216	0.81[JPT][hapmap]
rs465898	0.81[JPT][hapmap]
rs4705813	0.82[AMR][1000 genomes]
rs485210	0.84[MEX][hapmap]
rs492346	0.84[MEX][hapmap]
rs6594700	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs6594711	0.84[CEU][hapmap]
rs6869097	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6873400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6873755	0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6875238	0.82[AMR][1000 genomes]
rs6894434	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7702120	0.84[CEU][hapmap]
rs7719254	0.85[YRI][hapmap]
rs7722276	0.85[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs7735247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4705812	YTHDC2	cis	cerebellum	SCAN
rs4705812	LILRP2	trans	parietal	SCAN
rs4705812	YTHDC2	cis	parietal	SCAN

Chromatin state (count:21 , 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	chr5:112672000-112674600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:112672000-112674600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:112672800-112675000	Enhancers	Ovary	ovary
14	chr5:112673000-112676400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:112673200-112675000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr5:112673200-112676800	Weak transcription	Fetal Stomach	stomach
17	chr5:112673200-112678400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:112673800-112675400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:112674200-112676000	Enhancers	Fetal Heart	heart
20	chr5:112674200-112676200	Weak transcription	Left Ventricle	heart
21	chr5:112674400-112676200	Weak transcription	Right Atrium	heart

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