Variant report

Variant	rs1734622
Chromosome Location	chr19:44959866-44959867
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1865385	1.00[ASN][1000 genomes]
rs204527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204529	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204532	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204542	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204548	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204550	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs204553	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs204554	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs204556	1.00[ASN][1000 genomes]
rs2117384	0.88[CEU][hapmap]
rs2571041	1.00[ASN][1000 genomes]
rs2571048	0.80[CEU][hapmap]
rs2571050	0.88[CEU][hapmap]
rs2571053	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2571059	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2686756	1.00[ASN][1000 genomes]
rs2686757	1.00[ASN][1000 genomes]
rs2686758	0.81[CEU][hapmap]
rs2686769	1.00[ASN][1000 genomes]
rs431273	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62118147	1.00[ASN][1000 genomes]
rs629579	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8107008	1.00[CHB][hapmap]
rs926020	0.80[CEU][hapmap]
rs930462	1.00[CHB][hapmap]
rs954314	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv579858	chr19:44955927-44962865	ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1814695	chr19:44955927-44963056	ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv524201	chr19:44955927-44978183	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv525472	chr19:44955927-44978183	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv16834	chr19:44957502-44964253	Weak transcription ZNF genes & repeats Active TSS Enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases
9	nsv912115	chr19:44957508-44995990	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	esv7164	chr19:44957517-44963854	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases
11	nsv512583	chr19:44957523-44962575	ZNF genes & repeats Weak transcription Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases
12	esv3319150	chr19:44957559-44963817	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases
13	esv3319152	chr19:44957777-44963902	ZNF genes & repeats Weak transcription Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
14	nsv579859	chr19:44957908-44962424	Active TSS ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	diseases
15	esv1809209	chr19:44957908-44963056	ZNF genes & repeats Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
16	esv3401656	chr19:44958072-44963810	Weak transcription ZNF genes & repeats Active TSS Enhancers	n/a	n/a	inside rSNPs	diseases
17	esv1794604	chr19:44958384-44959866	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
18	esv1805233	chr19:44958384-44962865	ZNF genes & repeats Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
19	nsv579860	chr19:44958384-44962865	ZNF genes & repeats Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
20	nsv960853	chr19:44958445-44982821	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1734622	ZNF180	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44959000-44960000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr19:44959800-44961000	Weak transcription	Adipose Nuclei	Adipose
3	chr19:44959800-44961000	Weak transcription	Brain Hippocampus Middle	brain
4	chr19:44959800-44961200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr19:44959800-44961200	Weak transcription	Colon Smooth Muscle	Colon
6	chr19:44959800-44961200	Weak transcription	Stomach Mucosa	stomach

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