Variant report

Variant	rs2571042
Chromosome Location	chr19:44986702-44986703
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1897820	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1897823	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1996823	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2117384	0.81[MEX][hapmap]
rs2253210	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2253563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2461534	0.85[AFR][1000 genomes]
rs2571043	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571046	0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs2571047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571048	0.87[LWK][hapmap];0.81[MEX][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs2571049	0.85[AFR][1000 genomes]
rs2571051	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2571052	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2571108	0.84[GIH][hapmap]
rs2686758	0.85[AFR][1000 genomes]
rs2686760	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686763	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686764	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686779	0.82[GIH][hapmap]
rs28410042	0.81[ASN][1000 genomes]
rs4803714	0.83[ASW][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6509162	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs926020	0.87[LWK][hapmap];0.81[MEX][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2571042	TMEM143	cis	parietal	SCAN
rs2571042	NAPSA	cis	parietal	SCAN
rs2571042	CCDC8	cis	parietal	SCAN
rs2571042	NUCB1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

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	chr19:44972600-44992200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
6	chr19:44975200-44992200	ZNF genes & repeats	Fetal Brain Female	brain
7	chr19:44975400-44992200	ZNF genes & repeats	Brain Hippocampus Middle	brain
8	chr19:44975600-44990000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:44975600-44992200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
10	chr19:44975800-44992200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
11	chr19:44975800-44992200	ZNF genes & repeats	Brain Anterior Caudate	brain
12	chr19:44976000-44992400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
13	chr19:44976400-44992000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:44976400-44992000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
15	chr19:44976600-44992000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
16	chr19:44976600-44992200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
17	chr19:44976600-44992200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
18	chr19:44976600-44992400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
19	chr19:44977000-44989800	ZNF genes & repeats	Brain Angular Gyrus	brain
20	chr19:44977000-44990200	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
21	chr19:44977000-44992000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:44977000-44992200	ZNF genes & repeats	Brain Cingulate Gyrus	brain
23	chr19:44977000-44992200	ZNF genes & repeats	Brain Substantia Nigra	brain
24	chr19:44977000-44992400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr19:44977000-44992400	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
26	chr19:44977200-44987600	ZNF genes & repeats	Left Ventricle	heart
27	chr19:44977200-44991800	ZNF genes & repeats	Colon Smooth Muscle	Colon
28	chr19:44977200-44992000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
29	chr19:44977200-44992000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
30	chr19:44977200-44992200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
31	chr19:44977200-44992800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:44977400-44987600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:44977400-44989600	ZNF genes & repeats	Right Ventricle	heart
34	chr19:44977400-44990000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:44977400-44992000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
36	chr19:44977400-44992200	ZNF genes & repeats	Fetal Lung	lung
37	chr19:44977400-44992400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
38	chr19:44977400-44992400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:44977600-44989800	ZNF genes & repeats	Ovary	ovary
40	chr19:44977600-44992000	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr19:44977600-44992200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:44977800-44989200	ZNF genes & repeats	NH-A	brain
43	chr19:44977800-44989600	ZNF genes & repeats	Fetal Brain Male	brain
44	chr19:44977800-44992000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr19:44977800-44992000	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr19:44977800-44992200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:44977800-44992200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:44977800-44992600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
49	chr19:44977800-44992600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
50	chr19:44977800-44992600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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