Variant report

Variant	rs1996823
Chromosome Location	chr19:44978453-44978454
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44763163..44765702-chr19:44978103..44979674,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159915	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1897820	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1897823	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1897824	0.83[AFR][1000 genomes]
rs2253210	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253563	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][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]
rs2571042	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]
rs2571043	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[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];0.96[ASN][1000 genomes]
rs2571045	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571047	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2571051	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571052	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2571108	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs2686760	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686763	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686764	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2686765	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2686779	0.82[GIH][hapmap]
rs28410042	0.85[ASN][1000 genomes]
rs4803714	0.89[LWK][hapmap];0.86[YRI][hapmap]
rs6509162	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	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
6	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1996823	LIM2	cis	cerebellum	SCAN
rs1996823	ZNF432	cis	cerebellum	SCAN
rs1996823	NAPSA	cis	parietal	SCAN
rs1996823	GRWD1	cis	cerebellum	SCAN
rs1996823	SLC17A7	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

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	chr19:44977200-44979200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:44977200-44979800	ZNF genes & repeats	Colonic Mucosa	Colon
28	chr19:44977200-44987600	ZNF genes & repeats	Left Ventricle	heart
29	chr19:44977200-44991800	ZNF genes & repeats	Colon Smooth Muscle	Colon
30	chr19:44977200-44992000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
31	chr19:44977200-44992000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
32	chr19:44977200-44992200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
33	chr19:44977200-44992800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:44977400-44979200	ZNF genes & repeats	Gastric	stomach
35	chr19:44977400-44979600	ZNF genes & repeats	Aorta	Aorta
36	chr19:44977400-44979600	ZNF genes & repeats	Pancreas	Pancrea
37	chr19:44977400-44987600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:44977400-44989600	ZNF genes & repeats	Right Ventricle	heart
39	chr19:44977400-44990000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:44977400-44992000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
41	chr19:44977400-44992200	ZNF genes & repeats	Fetal Lung	lung
42	chr19:44977400-44992400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
43	chr19:44977400-44992400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:44977600-44981600	ZNF genes & repeats	Right Atrium	heart
45	chr19:44977600-44989800	ZNF genes & repeats	Ovary	ovary
46	chr19:44977600-44992000	ZNF genes & repeats	Primary T cells from cord blood	blood
47	chr19:44977600-44992200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:44977800-44979200	ZNF genes & repeats	Fetal Stomach	stomach
49	chr19:44977800-44989200	ZNF genes & repeats	NH-A	brain
50	chr19:44977800-44989600	ZNF genes & repeats	Fetal Brain Male	brain

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