Variant report

Variant	rs441549
Chromosome Location	chr19:53046279-53046280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs162277	0.82[EUR][1000 genomes]
rs162278	0.82[EUR][1000 genomes]
rs1676153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608513	0.91[ASN][1000 genomes]
rs2608522	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2608527	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2615586	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2615587	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2615588	0.94[ASN][1000 genomes]
rs2617795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2633502	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2633513	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633514	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2633517	0.85[ASN][1000 genomes]
rs2925976	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs326438	0.80[AMR][1000 genomes]
rs326439	0.94[ASN][1000 genomes]
rs326440	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs326441	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs326442	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs326443	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs326444	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs326446	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs326447	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326448	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs326458	0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs329967	0.86[GIH][hapmap]
rs368922	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs369806	0.80[EUR][1000 genomes]
rs375267	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376595	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs396663	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs400709	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs402737	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs410046	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs413751	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs413814	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs417599	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs422195	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs429367	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs434709	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs434788	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs439618	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs440545	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs441850	0.88[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs445500	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs449671	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4802971	0.87[ASN][1000 genomes]
rs4802972	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs520958	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs521703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs529698	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs532449	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs606521	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs606538	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs606914	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs607477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62117197	0.88[ASN][1000 genomes]
rs62117198	0.89[ASN][1000 genomes]
rs62117199	0.90[ASN][1000 genomes]
rs62119359	0.85[ASN][1000 genomes]
rs642493	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs653483	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs656541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs666356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs668882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs685200	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs688646	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs781129	0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs92520	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9676916	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs441549	SHISA7	cis	parietal	SCAN
rs441549	ZNF582	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53032200-53057000	Weak transcription	Hela-S3	cervix
2	chr19:53032600-53049800	Weak transcription	HepG2	liver
3	chr19:53037600-53051800	Weak transcription	K562	blood
4	chr19:53039000-53052200	Weak transcription	Fetal Brain Male	brain
5	chr19:53039200-53056000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
6	chr19:53039600-53052000	Weak transcription	HSMMtube	muscle
7	chr19:53039800-53050600	Weak transcription	Fetal Lung	lung
8	chr19:53039800-53051600	Weak transcription	Brain Substantia Nigra	brain
9	chr19:53039800-53051600	Weak transcription	Fetal Kidney	kidney
10	chr19:53040000-53046600	Weak transcription	Gastric	stomach
11	chr19:53040000-53046600	Weak transcription	Ovary	ovary
12	chr19:53040000-53046800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:53040000-53046800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr19:53040000-53046800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:53040000-53046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:53040000-53047400	Weak transcription	Brain Hippocampus Middle	brain
17	chr19:53040000-53047400	Weak transcription	HSMM	muscle
18	chr19:53040000-53047600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:53040000-53051600	Weak transcription	Brain Angular Gyrus	brain
20	chr19:53040000-53051800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:53040000-53052000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:53040000-53052200	Weak transcription	Psoas Muscle	Psoas
23	chr19:53040000-53054400	Weak transcription	Fetal Heart	heart
24	chr19:53040200-53046400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:53040200-53046400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:53040200-53046600	Weak transcription	Osteobl	bone
27	chr19:53040200-53046800	Weak transcription	Right Ventricle	heart
28	chr19:53040200-53047400	Weak transcription	Fetal Brain Female	brain
29	chr19:53040200-53050000	Weak transcription	Colon Smooth Muscle	Colon
30	chr19:53040200-53051800	Weak transcription	NHDF-Ad	bronchial
31	chr19:53040200-53057400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:53040400-53046400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr19:53040400-53046400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:53040400-53046400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr19:53040400-53046600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr19:53040400-53046600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr19:53040400-53046600	Weak transcription	Adipose Nuclei	Adipose
38	chr19:53040400-53046600	Weak transcription	HMEC	breast
39	chr19:53040400-53046600	Weak transcription	NHLF	lung
40	chr19:53040400-53046800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:53040400-53046800	Weak transcription	Primary T cells from cord blood	blood
42	chr19:53040400-53046800	Weak transcription	Brain Germinal Matrix	brain
43	chr19:53040400-53046800	Weak transcription	Placenta	Placenta
44	chr19:53040400-53047000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:53040400-53057600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:53040600-53046800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr19:53040600-53047400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:53040600-53049800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr19:53042000-53070400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:53042200-53051600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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