Variant report

Variant	rs13228
Chromosome Location	chr19:39669642-39669643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39668971..39672206-chr19:39672666..39676660,4	K562	blood:
2	chr19:39460475..39462812-chr19:39669230..39671981,2	K562	blood:
3	chr19:39602450..39604477-chr19:39669469..39671125,2	K562	blood:
4	chr19:39661354..39664969-chr19:39667495..39672499,5	MCF-7	breast:
5	chr19:39660751..39662815-chr19:39667142..39670413,4	K562	blood:
6	chr19:39621851..39624607-chr19:39667898..39670113,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11083508	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs11666140	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11666238	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11669124	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs11671084	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs11672886	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs11673014	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs12972566	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17641276	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs17708461	0.92[CEU][hapmap]
rs2304090	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2319152	0.81[EUR][1000 genomes]
rs2319153	0.88[ASN][1000 genomes]
rs35946542	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803209	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs59944493	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71334840	0.91[ASN][1000 genomes]
rs750247	0.95[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs754703	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs754704	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8101281	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs8101444	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs874535	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs879689	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.82[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13228	PAK4	cis	Skin Sun Exposed Lower leg	GTEx
rs13228	PAK4	cis	Whole Blood	GTEx
rs13228	ENSG00000130669	cis	multi-tissue	Pritchard
rs13228	PAK4	cis	Thyroid	GTEx
rs13228	PAK4	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
2	chr19:39647800-39670400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr19:39654200-39674000	Weak transcription	K562	blood
4	chr19:39657800-39687600	Weak transcription	Right Atrium	heart
5	chr19:39658400-39670800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr19:39658400-39673000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr19:39658800-39672400	Strong transcription	Colonic Mucosa	Colon
8	chr19:39658800-39673000	Strong transcription	Fetal Intestine Small	intestine
9	chr19:39659000-39669800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr19:39659000-39670000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:39659000-39670800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:39659000-39671200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:39659000-39671600	Strong transcription	Thymus	Thymus
14	chr19:39659000-39672000	Weak transcription	HMEC	breast
15	chr19:39659000-39672800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:39659200-39671000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:39659200-39672400	Strong transcription	Fetal Intestine Large	intestine
18	chr19:39659200-39672400	Strong transcription	Stomach Smooth Muscle	stomach
19	chr19:39659200-39672800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:39659400-39671200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:39659400-39672000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:39659400-39672000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr19:39659400-39672200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:39659400-39672600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:39659400-39672800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:39659400-39673200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:39659600-39670600	Strong transcription	NHLF	lung
28	chr19:39659600-39672800	Strong transcription	Brain Germinal Matrix	brain
29	chr19:39659600-39672800	Strong transcription	Placenta	Placenta
30	chr19:39659600-39673000	Strong transcription	Fetal Brain Female	brain
31	chr19:39659800-39669800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr19:39660000-39669800	Strong transcription	Right Ventricle	heart
33	chr19:39660000-39670800	Strong transcription	Ovary	ovary
34	chr19:39660000-39671600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr19:39660000-39673000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:39660400-39670800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr19:39660400-39672000	Strong transcription	Pancreas	Pancrea
38	chr19:39660600-39670600	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr19:39660600-39671000	Strong transcription	Liver	Liver
40	chr19:39660600-39671000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr19:39660600-39671000	Strong transcription	Dnd41	blood
42	chr19:39660800-39671600	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr19:39661400-39671000	Strong transcription	Spleen	Spleen
44	chr19:39661400-39672400	Strong transcription	Lung	lung
45	chr19:39661400-39673000	Strong transcription	Gastric	stomach
46	chr19:39661400-39684600	Weak transcription	HSMM	muscle
47	chr19:39661800-39671000	Strong transcription	Esophagus	oesophagus
48	chr19:39661800-39672000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr19:39661800-39673000	Strong transcription	Fetal Muscle Leg	muscle
50	chr19:39661800-39674000	Weak transcription	Stomach Mucosa	stomach

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