Variant report

Variant	rs1897823
Chromosome Location	chr19:44977240-44977241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1897820	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1897824	0.83[AFR][1000 genomes]
rs1996823	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2117384	0.81[MEX][hapmap]
rs2253210	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2253563	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2571042	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2571043	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2571045	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2571047	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2571048	0.81[MEX][hapmap]
rs2571051	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2571052	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571056	0.81[CEU][hapmap]
rs2571108	0.84[GIH][hapmap]
rs2686760	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2686763	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2686764	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2686765	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2686779	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs28410042	0.95[ASN][1000 genomes]
rs4803714	0.89[LWK][hapmap];0.83[YRI][hapmap]
rs6509162	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs926020	0.81[MEX][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1897823	KDELR1	cis	cerebellum	SCAN
rs1897823	KLK3	cis	cerebellum	SCAN
rs1897823	ZNF432	cis	cerebellum	SCAN
rs1897823	RTN2	cis	cerebellum	SCAN
rs1897823	GRWD1	cis	cerebellum	SCAN
rs1897823	SIGLEC9	cis	cerebellum	SCAN
rs1897823	PTOV1	cis	cerebellum	SCAN

Chromatin state (count:35 , 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
27	chr19:44977200-44978400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:44977200-44979200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:44977200-44979800	ZNF genes & repeats	Colonic Mucosa	Colon
30	chr19:44977200-44987600	ZNF genes & repeats	Left Ventricle	heart
31	chr19:44977200-44991800	ZNF genes & repeats	Colon Smooth Muscle	Colon
32	chr19:44977200-44992000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
33	chr19:44977200-44992000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
34	chr19:44977200-44992200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
35	chr19:44977200-44992800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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