Variant report

Variant	rs691080
Chromosome Location	chr19:39647284-39647285
allele	A/G
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	EGR1	chr19:39647166-39647406	K562	blood:	n/a	chr19:39647251-39647261 chr19:39647174-39647184
2	MYC	chr19:39647244-39647330	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:39647275-39647436	MCF-7	breast:	n/a	n/a
4	MAX	chr19:39646955-39647811	MCF-7	breast:	n/a	chr19:39647210-39647220 chr19:39647210-39647221 chr19:39647210-39647221 chr19:39647209-39647222 chr19:39647211-39647221 chr19:39647209-39647222 chr19:39647206-39647225 chr19:39647211-39647220 chr19:39647210-39647221 chr19:39647210-39647220 chr19:39647209-39647222 chr19:39647211-39647221
5	EGR1	chr19:39647111-39647475	K562	blood:	n/a	chr19:39647251-39647261 chr19:39647463-39647472 chr19:39647174-39647184
6	ELF1	chr19:39647267-39647573	K562	blood:	n/a	n/a
7	MAZ	chr19:39647020-39648140	IMR90	lung:	n/a	chr19:39647210-39647220 chr19:39647210-39647221 chr19:39647210-39647221 chr19:39647209-39647222 chr19:39647211-39647221 chr19:39647209-39647222 chr19:39647206-39647225 chr19:39647211-39647220 chr19:39647210-39647221 chr19:39647210-39647220 chr19:39647209-39647222 chr19:39647211-39647221

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39645610..39647317-chr19:39897484..39899400,2	MCF-7	breast:
2	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:

Variant related genes	Relation type
PAK4	TF binding region
ENSG00000130669	Chromatin interaction
ENSG00000269172	Chromatin interaction
ENSG00000128016	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12976130	0.85[EUR][1000 genomes]
rs12976664	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12977799	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1549927	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs476713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803208	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs490249	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513053	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs529336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs550664	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs554114	0.84[EUR][1000 genomes]
rs576527	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs691577	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs692191	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs692257	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs692337	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs692468	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692475	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs691080	PAK4	cis	Thyroid	GTEx

Chromatin state (count:111 , 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	chr19:39635600-39647400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr19:39636000-39647400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
7	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
8	chr19:39636800-39650800	Weak transcription	HUVEC	blood vessel
9	chr19:39637000-39653600	Weak transcription	Brain Germinal Matrix	brain
10	chr19:39637400-39647400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:39638200-39648600	Weak transcription	Brain Angular Gyrus	brain
14	chr19:39640000-39647600	Weak transcription	HSMMtube	muscle
15	chr19:39640000-39648400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
17	chr19:39640200-39647400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:39640200-39647400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:39640200-39660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:39641200-39649200	Weak transcription	Fetal Brain Female	brain
21	chr19:39642000-39649600	Enhancers	Placenta	Placenta
22	chr19:39642200-39647400	Weak transcription	Right Atrium	heart
23	chr19:39642400-39649000	Weak transcription	Thymus	Thymus
24	chr19:39643400-39648200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:39644200-39652200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr19:39644400-39647400	Enhancers	Liver	Liver
27	chr19:39644400-39648800	Enhancers	Gastric	stomach
28	chr19:39644400-39649600	Enhancers	Pancreas	Pancrea
29	chr19:39644400-39651800	Genic enhancers	Fetal Intestine Small	intestine
30	chr19:39644600-39647400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr19:39644600-39647800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr19:39644600-39647800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:39644600-39648400	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr19:39644600-39648600	Enhancers	Duodenum Mucosa	Duodenum
35	chr19:39644600-39648600	Enhancers	Fetal Heart	heart
36	chr19:39644600-39649000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:39644600-39649400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr19:39644600-39649400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:39644600-39649400	Enhancers	Lung	lung
40	chr19:39644600-39649600	Enhancers	K562	blood
41	chr19:39644600-39649800	Enhancers	Fetal Intestine Large	intestine
42	chr19:39644600-39652200	Enhancers	Stomach Mucosa	stomach
43	chr19:39644800-39647400	Enhancers	Fetal Muscle Trunk	muscle
44	chr19:39644800-39647800	Enhancers	Fetal Thymus	thymus
45	chr19:39644800-39647800	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr19:39644800-39648600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr19:39644800-39648600	Enhancers	Fetal Lung	lung
48	chr19:39644800-39652400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:39645000-39647600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr19:39645000-39647800	Enhancers	A549	lung

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