Variant report

Variant	rs12670798
Chromosome Location	chr7:21607352-21607353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10950855	0.81[LWK][hapmap]
rs10950856	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12667186	0.90[ASN][1000 genomes]
rs12670286	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs2177519	0.94[MEX][hapmap]
rs3810897	0.81[CEU][hapmap];0.84[CHD][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs3924043	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4294086	0.86[YRI][hapmap]
rs4374884	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4392792	0.80[LWK][hapmap]
rs4470903	0.82[EUR][1000 genomes]
rs4607494	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4639414	0.80[CEU][hapmap]
rs5008148	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55649657	0.83[EUR][1000 genomes]
rs55696093	0.83[EUR][1000 genomes]
rs56130071	0.82[EUR][1000 genomes]
rs56160141	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58243822	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs59509802	0.84[EUR][1000 genomes]
rs66476925	0.83[EUR][1000 genomes]
rs67449539	0.91[EUR][1000 genomes]
rs68042167	0.84[EUR][1000 genomes]
rs6970667	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6978629	0.81[LWK][hapmap]
rs73066466	0.84[EUR][1000 genomes]
rs73066481	0.83[EUR][1000 genomes]
rs73066485	0.83[EUR][1000 genomes]
rs73066492	0.91[ASN][1000 genomes]
rs7809080	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027302	chr7:21391598-21727016	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv538800	chr7:21391598-21727016	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1028434	chr7:21468437-21636671	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1023655	chr7:21486485-21727016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv538801	chr7:21486485-21727016	ZNF genes & repeats Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv830921	chr7:21489100-21688016	Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1030577	chr7:21548909-21681379	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv1025634	chr7:21566727-21686272	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv933452	chr7:21603688-21609638	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:6)

Disease	PMID	Source
Cholesterol, total	19060911	GWAS catalog
LDL cholesterol	24097068	GWAS catalog
LDL cholesterol	20686565	GWAS catalog
Cholesterol, total	20686565	GWAS catalog
Cholesterol, total	24097068	GWAS catalog
LDL cholesterol	19060911	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12670798	DNAH11	cis	multi-tissue	Pritchard
rs12670798	KLHL7	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:21591400-21610600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr7:21591400-21610600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:21591400-21627000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:21599400-21608600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:21601800-21622600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr7:21606000-21608000	Enhancers	Liver	Liver

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