Variant report

Variant	rs1897824
Chromosome Location	chr19:44977071-44977072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10401549	0.93[ASN][1000 genomes]
rs10402815	0.93[ASN][1000 genomes]
rs10402981	1.00[JPT][hapmap]
rs10406819	0.93[ASN][1000 genomes]
rs10407028	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10407556	1.00[JPT][hapmap]
rs10407887	0.93[ASN][1000 genomes]
rs10421647	0.98[ASN][1000 genomes]
rs13345032	1.00[JPT][hapmap]
rs1465723	1.00[JPT][hapmap]
rs16959164	0.88[JPT][hapmap]
rs16979124	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16979130	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16979134	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16979139	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16979226	0.86[JPT][hapmap]
rs1865385	0.92[EUR][1000 genomes]
rs1897820	0.82[AFR][1000 genomes]
rs1897821	0.95[EUR][1000 genomes]
rs1897822	0.88[ASN][1000 genomes]
rs1897823	0.83[AFR][1000 genomes]
rs1996823	0.80[YRI][hapmap];0.83[AFR][1000 genomes]
rs204530	0.92[CEU][hapmap]
rs2117384	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2140112	0.93[ASN][1000 genomes]
rs2253210	0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs2461534	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2571040	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2571041	0.94[EUR][1000 genomes]
rs2571046	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2571048	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2571049	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2571050	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2571051	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs2571052	0.83[AFR][1000 genomes]
rs2571053	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2571059	0.91[EUR][1000 genomes]
rs2571115	0.81[EUR][1000 genomes]
rs2571116	0.84[EUR][1000 genomes]
rs2686756	0.94[EUR][1000 genomes]
rs2686757	0.94[EUR][1000 genomes]
rs2686758	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2686762	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2686769	0.82[EUR][1000 genomes]
rs28428189	0.93[ASN][1000 genomes]
rs28507279	0.93[ASN][1000 genomes]
rs28576758	0.93[ASN][1000 genomes]
rs3786496	1.00[JPT][hapmap]
rs4297799	0.98[ASN][1000 genomes]
rs56787156	0.93[ASN][1000 genomes]
rs62118145	0.83[EUR][1000 genomes]
rs629579	0.91[EUR][1000 genomes]
rs7250221	0.93[EUR][1000 genomes]
rs926020	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs954314	0.96[CEU][hapmap];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	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
7	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
8	nsv978867	chr19:44963452-44982821	ZNF genes & repeats Strong transcription Weak transcription Active TSS	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
rs1897824	ZNF180	cis	Muscle Skeletal	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44966800-44992400	ZNF genes & repeats	Liver	Liver
2	chr19:44967200-44992800	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:44969800-44992200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:44971600-44992200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:44972400-44977600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:44972600-44992200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
7	chr19:44975200-44992200	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:44975400-44992200	ZNF genes & repeats	Brain Hippocampus Middle	brain
9	chr19:44975600-44990000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:44975600-44992200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
11	chr19:44975800-44992200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
12	chr19:44975800-44992200	ZNF genes & repeats	Brain Anterior Caudate	brain
13	chr19:44976000-44992400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr19:44976400-44992000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:44976400-44992000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
16	chr19:44976600-44992000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
17	chr19:44976600-44992200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr19:44976600-44992200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
19	chr19:44976600-44992400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
20	chr19:44977000-44989800	ZNF genes & repeats	Brain Angular Gyrus	brain
21	chr19:44977000-44990200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
22	chr19:44977000-44992000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:44977000-44992200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
24	chr19:44977000-44992200	ZNF genes & repeats	Brain Substantia Nigra	brain
25	chr19:44977000-44992400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
26	chr19:44977000-44992400	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood

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