Variant report

Variant	rs12977799
Chromosome Location	chr19:39661388-39661389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39660565-39661810	PANC-1	pancreas:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39661354..39664969-chr19:39667495..39672499,5	MCF-7	breast:
2	chr19:39660707..39662756-chr19:39672502..39674103,2	K562	blood:
3	chr19:39656758..39659351-chr19:39659366..39664473,5	MCF-7	breast:
4	chr19:39660751..39662815-chr19:39667142..39670413,4	K562	blood:
5	chr19:39660731..39663212-chr19:39664452..39666309,2	K562	blood:

No data

Variant related genes	Relation type
PAK4	TF binding region
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12976130	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12976664	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549927	0.85[EUR][1000 genomes]
rs476713	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803208	0.83[EUR][1000 genomes]
rs490249	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs513053	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs529336	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs550664	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs576527	0.90[EUR][1000 genomes]
rs691080	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs691577	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs692191	0.83[EUR][1000 genomes]
rs692257	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs692337	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs692468	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs692475	0.92[EUR][1000 genomes];0.91[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12977799	PAK4	cis	Thyroid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
2	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
3	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
5	chr19:39647600-39664800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr19:39647800-39670400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:39653800-39663200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:39654000-39661400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:39654200-39674000	Weak transcription	K562	blood
10	chr19:39656600-39664800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:39657200-39667200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr19:39657800-39663000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:39657800-39687600	Weak transcription	Right Atrium	heart
14	chr19:39658000-39661400	Weak transcription	Brain Substantia Nigra	brain
15	chr19:39658000-39666600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:39658400-39665600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:39658400-39665600	Strong transcription	Fetal Stomach	stomach
18	chr19:39658400-39670800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:39658400-39673000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:39658600-39662400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:39658800-39663200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr19:39658800-39663200	Weak transcription	NHEK	skin
23	chr19:39658800-39672400	Strong transcription	Colonic Mucosa	Colon
24	chr19:39658800-39673000	Strong transcription	Fetal Intestine Small	intestine
25	chr19:39659000-39669800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr19:39659000-39670000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:39659000-39670800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:39659000-39671200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:39659000-39671600	Strong transcription	Thymus	Thymus
30	chr19:39659000-39672000	Weak transcription	HMEC	breast
31	chr19:39659000-39672800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:39659200-39661800	Strong transcription	Brain Cingulate Gyrus	brain
33	chr19:39659200-39671000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:39659200-39672400	Strong transcription	Fetal Intestine Large	intestine
35	chr19:39659200-39672400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:39659200-39672800	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:39659400-39661400	Genic enhancers	Lung	lung
38	chr19:39659400-39662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:39659400-39665000	Weak transcription	Fetal Lung	lung
40	chr19:39659400-39669400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr19:39659400-39671200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:39659400-39672000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:39659400-39672000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:39659400-39672200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:39659400-39672600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr19:39659400-39672800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr19:39659400-39673200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:39659600-39662200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:39659600-39670600	Strong transcription	NHLF	lung
50	chr19:39659600-39672800	Strong transcription	Brain Germinal Matrix	brain

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