Variant report

Variant	rs1529712
Chromosome Location	chr19:39666967-39666968
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39666769-39666969	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:39666113-39668283	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39665715..39668088-chr19:39693870..39695722,2	K562	blood:

Variant related genes	Relation type
PAK4	TF binding region
ENSG00000179751	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11671084	0.84[CEU][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1529712	PAK4	cis	Adipose Subcutaneous	GTEx
rs1529712	B3GNT8	cis	cerebellum	SCAN
rs1529712	PAK4	cis	Skin Sun Exposed Lower leg	GTEx
rs1529712	CRX	cis	parietal	SCAN
rs1529712	PAK4	cis	Thyroid	GTEx

Chromatin state (count:116 , 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	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
3	chr19:39647800-39670400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:39654200-39674000	Weak transcription	K562	blood
5	chr19:39657200-39667200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:39657800-39687600	Weak transcription	Right Atrium	heart
7	chr19:39658400-39670800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:39658400-39673000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:39658800-39672400	Strong transcription	Colonic Mucosa	Colon
10	chr19:39658800-39673000	Strong transcription	Fetal Intestine Small	intestine
11	chr19:39659000-39669800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr19:39659000-39670000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:39659000-39670800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:39659000-39671200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:39659000-39671600	Strong transcription	Thymus	Thymus
16	chr19:39659000-39672000	Weak transcription	HMEC	breast
17	chr19:39659000-39672800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:39659200-39671000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr19:39659200-39672400	Strong transcription	Fetal Intestine Large	intestine
20	chr19:39659200-39672400	Strong transcription	Stomach Smooth Muscle	stomach
21	chr19:39659200-39672800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr19:39659400-39669400	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr19:39659400-39671200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:39659400-39672000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:39659400-39672000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr19:39659400-39672200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:39659400-39672600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:39659400-39672800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:39659400-39673200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:39659600-39670600	Strong transcription	NHLF	lung
31	chr19:39659600-39672800	Strong transcription	Brain Germinal Matrix	brain
32	chr19:39659600-39672800	Strong transcription	Placenta	Placenta
33	chr19:39659600-39673000	Strong transcription	Fetal Brain Female	brain
34	chr19:39659800-39669800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:39660000-39669600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:39660000-39669800	Strong transcription	Right Ventricle	heart
37	chr19:39660000-39670800	Strong transcription	Ovary	ovary
38	chr19:39660000-39671600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr19:39660000-39673000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:39660400-39670800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:39660400-39672000	Strong transcription	Pancreas	Pancrea
42	chr19:39660600-39669600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:39660600-39670600	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:39660600-39671000	Strong transcription	Liver	Liver
45	chr19:39660600-39671000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr19:39660600-39671000	Strong transcription	Dnd41	blood
47	chr19:39660800-39671600	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr19:39661400-39671000	Strong transcription	Spleen	Spleen
49	chr19:39661400-39672400	Strong transcription	Lung	lung
50	chr19:39661400-39673000	Strong transcription	Gastric	stomach

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