Variant report

Variant	rs1654351
Chromosome Location	chr19:38554725-38554726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1630393	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654346	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654353	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725471	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1725476	0.88[AFR][1000 genomes]
rs4803708	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249265	0.82[CHB][hapmap]
rs855635	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1062518	chr19:38540454-38564913	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1654351	ZNF780A	cis	cerebellum	SCAN
rs1654351	ZNF235	cis	parietal	SCAN
rs1654351	ZNF526	cis	cerebellum	SCAN
rs1654351	LYPD3	cis	parietal	SCAN
rs1654351	SIRT2	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
2	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
3	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
4	chr19:38543800-38563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr19:38547000-38554800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr19:38547000-38563600	Weak transcription	Fetal Lung	lung
8	chr19:38547200-38561400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:38548600-38555000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:38549200-38564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:38549200-38572000	Weak transcription	Liver	Liver
12	chr19:38549400-38560000	Weak transcription	Psoas Muscle	Psoas
13	chr19:38549600-38572600	Weak transcription	Thymus	Thymus
14	chr19:38550000-38561000	Weak transcription	Hela-S3	cervix
15	chr19:38550000-38570400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:38550800-38563400	Weak transcription	Spleen	Spleen
17	chr19:38550800-38565200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr19:38550800-38570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:38550800-38572200	Weak transcription	Colonic Mucosa	Colon
20	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr19:38551000-38556000	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr19:38551000-38572000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:38551200-38555600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:38551200-38562200	Weak transcription	Primary T cells from cord blood	blood
25	chr19:38551200-38562600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr19:38551200-38563600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr19:38551200-38567000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:38551400-38562400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:38551400-38567000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:38551600-38554800	Enhancers	HSMM	muscle
32	chr19:38551800-38555000	Enhancers	Fetal Muscle Leg	muscle
33	chr19:38552200-38555000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:38552200-38555000	Genic enhancers	Fetal Intestine Large	intestine
35	chr19:38552200-38556000	Strong transcription	Primary B cells from cord blood	blood
36	chr19:38552400-38560800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:38552400-38561000	Weak transcription	NHEK	skin
38	chr19:38552400-38561200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:38552600-38554800	Genic enhancers	Fetal Intestine Small	intestine
40	chr19:38552600-38555000	Enhancers	Fetal Muscle Trunk	muscle
41	chr19:38552600-38555400	Weak transcription	Osteobl	bone
42	chr19:38552600-38559800	Weak transcription	HSMMtube	muscle
43	chr19:38552800-38554800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:38552800-38560000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:38553000-38554800	Enhancers	Brain Angular Gyrus	brain
46	chr19:38553000-38559400	Strong transcription	A549	lung
47	chr19:38553000-38559600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr19:38553000-38559800	Weak transcription	NHDF-Ad	bronchial
49	chr19:38553200-38570400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:38553400-38554800	Enhancers	Ovary	ovary

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