Variant report

Variant	rs754703
Chromosome Location	chr19:39648322-39648323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130669	Chromatin interaction
ENSG00000269172	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11083508	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11666140	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666238	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11669124	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11672886	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11673014	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12972566	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13228	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17708461	0.81[EUR][1000 genomes]
rs2304090	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2319152	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35946542	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4273158	0.84[AMR][1000 genomes]
rs4611580	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4803209	0.81[EUR][1000 genomes]
rs4803212	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59944493	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs750247	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754704	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8101281	0.81[EUR][1000 genomes]
rs8101444	0.81[ASN][1000 genomes]
rs8105289	0.85[ASN][1000 genomes]
rs874535	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs879689	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3403825	chr19:39646612-39650810	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs754703	PAK4	cis	Adipose Subcutaneous	GTEx
rs754703	PAK4	cis	Skin Sun Exposed Lower leg	GTEx
rs754703	PAK4	cis	Whole Blood	GTEx
rs754703	PAK4	cis	Thyroid	GTEx

Chromatin state (count:109 , 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	chr19:39630800-39651000	Weak transcription	NHDF-Ad	bronchial
3	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
5	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
6	chr19:39636800-39650800	Weak transcription	HUVEC	blood vessel
7	chr19:39637000-39653600	Weak transcription	Brain Germinal Matrix	brain
8	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:39638200-39648600	Weak transcription	Brain Angular Gyrus	brain
11	chr19:39640000-39648400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
13	chr19:39640200-39660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:39641200-39649200	Weak transcription	Fetal Brain Female	brain
15	chr19:39642000-39649600	Enhancers	Placenta	Placenta
16	chr19:39642400-39649000	Weak transcription	Thymus	Thymus
17	chr19:39644200-39652200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr19:39644400-39648800	Enhancers	Gastric	stomach
19	chr19:39644400-39649600	Enhancers	Pancreas	Pancrea
20	chr19:39644400-39651800	Genic enhancers	Fetal Intestine Small	intestine
21	chr19:39644600-39648400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr19:39644600-39648600	Enhancers	Duodenum Mucosa	Duodenum
23	chr19:39644600-39648600	Enhancers	Fetal Heart	heart
24	chr19:39644600-39649000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:39644600-39649400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr19:39644600-39649400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:39644600-39649400	Enhancers	Lung	lung
28	chr19:39644600-39649600	Enhancers	K562	blood
29	chr19:39644600-39649800	Enhancers	Fetal Intestine Large	intestine
30	chr19:39644600-39652200	Enhancers	Stomach Mucosa	stomach
31	chr19:39644800-39648600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr19:39644800-39648600	Enhancers	Fetal Lung	lung
33	chr19:39644800-39652400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:39645200-39648600	Weak transcription	Brain Substantia Nigra	brain
35	chr19:39645200-39659000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr19:39645400-39649600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr19:39645400-39654600	Enhancers	Ovary	ovary
38	chr19:39645600-39648400	Weak transcription	Brain Hippocampus Middle	brain
39	chr19:39645800-39658000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr19:39646000-39649000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:39646000-39649000	Enhancers	Left Ventricle	heart
42	chr19:39646600-39649400	Enhancers	Right Ventricle	heart
43	chr19:39646600-39652200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:39646600-39653200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:39646600-39659000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:39646800-39648600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr19:39646800-39659200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr19:39646800-39660600	Weak transcription	Dnd41	blood
49	chr19:39647000-39648400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:39647000-39648600	Flanking Active TSS	Stomach Smooth Muscle	stomach

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