Variant report

Variant	rs59944493
Chromosome Location	chr19:39636597-39636598
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39630404..39632300-chr19:39634611..39637101,2	MCF-7	breast:
2	chr19:39635749..39637767-chr19:39638007..39640559,2	K562	blood:
3	chr19:39633693..39637840-chr19:39657942..39661020,3	MCF-7	breast:
4	chr19:39635690..39638303-chr19:39642762..39645272,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11083508	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11666140	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11666238	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11669124	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11672886	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673014	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972566	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13228	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17708461	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2304090	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2319152	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35946542	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4273158	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4611580	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4803207	0.81[EUR][1000 genomes]
rs4803209	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4803212	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750247	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs754703	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs754704	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8101281	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8105289	0.81[ASN][1000 genomes]
rs874535	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs879689	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[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	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs59944493	PAK4	cis	Whole Blood	GTEx
rs59944493	PAK4	cis	Thyroid	GTEx
rs59944493	PAK4	cis	Adipose Subcutaneous	GTEx
rs59944493	PAK4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
3	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr19:39622600-39639600	Weak transcription	HSMM	muscle
5	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:39624000-39647000	Weak transcription	NHLF	lung
7	chr19:39627200-39646800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:39627600-39641200	Weak transcription	Hela-S3	cervix
9	chr19:39627600-39645800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr19:39629200-39639400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:39629600-39637600	Genic enhancers	Fetal Intestine Small	intestine
12	chr19:39630800-39646800	Weak transcription	Osteobl	bone
13	chr19:39630800-39651000	Weak transcription	NHDF-Ad	bronchial
14	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:39631200-39637200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:39631800-39639400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr19:39631800-39640800	Weak transcription	K562	blood
18	chr19:39631800-39644600	Weak transcription	Primary T cells from cord blood	blood
19	chr19:39632600-39637400	Enhancers	Primary hematopoietic stem cells	blood
20	chr19:39633000-39637400	Enhancers	Placenta	Placenta
21	chr19:39634400-39637400	Enhancers	Duodenum Mucosa	Duodenum
22	chr19:39634600-39636800	Enhancers	HUVEC	blood vessel
23	chr19:39634600-39637000	Enhancers	Fetal Lung	lung
24	chr19:39634600-39637000	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr19:39634600-39637400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:39634600-39638200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr19:39634800-39636800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:39634800-39636800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:39634800-39636800	Enhancers	Fetal Brain Male	brain
30	chr19:39634800-39636800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr19:39634800-39636800	Enhancers	HMEC	breast
32	chr19:39634800-39637000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:39634800-39637000	Enhancers	Placenta Amnion	Placenta Amnion
34	chr19:39634800-39637000	Enhancers	Right Atrium	heart
35	chr19:39634800-39637000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr19:39634800-39637200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr19:39634800-39637200	Enhancers	Fetal Muscle Leg	muscle
38	chr19:39634800-39637400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:39634800-39637400	Enhancers	Lung	lung
40	chr19:39634800-39637400	Enhancers	Pancreas	Pancrea
41	chr19:39634800-39637400	Enhancers	Stomach Mucosa	stomach
42	chr19:39634800-39637600	Enhancers	Fetal Heart	heart
43	chr19:39634800-39637600	Enhancers	Ovary	ovary
44	chr19:39634800-39637800	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr19:39634800-39638400	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr19:39634800-39638400	Enhancers	H1 Cell Line	embryonic stem cell
47	chr19:39634800-39638400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr19:39634800-39638400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr19:39634800-39638400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:39635000-39636800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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