Variant report

Variant	rs6453970
Chromosome Location	chr6:77993870-77993871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1342632	0.83[ASN][1000 genomes]
rs1361760	0.83[EUR][1000 genomes]
rs16888809	0.81[ASN][1000 genomes]
rs1970540	0.87[EUR][1000 genomes]
rs2211407	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211409	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211412	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2226149	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2320295	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35405235	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4499895	0.87[ASN][1000 genomes]
rs4708328	0.84[ASN][1000 genomes]
rs4708329	0.87[ASN][1000 genomes]
rs4708330	0.87[ASN][1000 genomes]
rs58535979	0.87[ASN][1000 genomes]
rs58816934	0.87[ASN][1000 genomes]
rs60136329	0.94[ASN][1000 genomes]
rs61003419	0.96[ASN][1000 genomes]
rs6921367	0.85[EUR][1000 genomes]
rs6932428	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9294070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9343598	0.94[EUR][1000 genomes]
rs9352465	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9359260	0.92[EUR][1000 genomes]
rs9359261	0.95[EUR][1000 genomes]
rs9443399	0.99[ASN][1000 genomes]
rs9448071	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017082	chr6:77585310-78258237	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv534282	chr6:77764575-78351994	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1034979	chr6:77781244-78426249	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538324	chr6:77781244-78426249	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2753543	chr6:77791848-78059351	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1015307	chr6:77902559-78352291	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6453970	HTR1B	cis	cerebellum	SCAN
rs6453970	TTK	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:77990800-78000400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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