Variant report

Variant	rs874535
Chromosome Location	chr19:39627893-39627894
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39624151..39625876-chr19:39627199..39629585,2	K562	blood:
2	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:
3	chr19:39627514..39630051-chr19:39655173..39657511,2	MCF-7	breast:
4	chr19:39622591..39626006-chr19:39627126..39631368,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11083508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11666140	0.82[EUR][1000 genomes]
rs11666238	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11669124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671084	0.96[CEU][hapmap]
rs11672886	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11673014	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12327657	0.94[ASN][1000 genomes]
rs12972566	0.82[EUR][1000 genomes]
rs12978321	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13228	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs17641276	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs17708461	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304090	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2319152	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35946542	0.82[EUR][1000 genomes]
rs4273158	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4611580	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803207	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803212	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59944493	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs750247	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs754703	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs754704	0.82[EUR][1000 genomes]
rs8101281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879689	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	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
4	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs874535	PAK4	cis	Whole Blood	GTEx
rs874535	PAK4	cis	Adipose Subcutaneous	GTEx
rs874535	PAK4	cis	Skin Sun Exposed Lower leg	GTEx
rs874535	PAK4	cis	Thyroid	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617000-39630800	Weak transcription	Primary T cells from cord blood	blood
2	chr19:39617000-39635000	Weak transcription	Aorta	Aorta
3	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:39617800-39628600	Enhancers	Placenta	Placenta
5	chr19:39617800-39630200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
7	chr19:39618200-39628400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr19:39620000-39630000	Weak transcription	HepG2	liver
10	chr19:39621000-39628400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:39621400-39628000	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr19:39622200-39628200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr19:39622400-39629000	Weak transcription	NH-A	brain
14	chr19:39622400-39635200	Weak transcription	Fetal Brain Female	brain
15	chr19:39622600-39639600	Weak transcription	HSMM	muscle
16	chr19:39623000-39635200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr19:39623400-39629000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:39623600-39630200	Weak transcription	Brain Angular Gyrus	brain
20	chr19:39623800-39630200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr19:39624000-39647000	Weak transcription	NHLF	lung
22	chr19:39624200-39629000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:39624200-39630200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:39624200-39634800	Weak transcription	Fetal Kidney	kidney
25	chr19:39624400-39628200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr19:39624400-39628600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:39624400-39629000	Weak transcription	Right Ventricle	heart
28	chr19:39624400-39629000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr19:39624400-39629200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:39624400-39630200	Weak transcription	Liver	Liver
31	chr19:39624600-39628600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:39624600-39629000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:39624600-39629000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:39624600-39630200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:39624800-39628600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:39624800-39629200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:39624800-39629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:39624800-39629600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:39624800-39629600	Weak transcription	Left Ventricle	heart
40	chr19:39624800-39632600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr19:39624800-39633000	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr19:39625000-39629800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:39625000-39630000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:39625200-39629000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr19:39625400-39628200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr19:39625600-39628400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:39625800-39629800	Weak transcription	K562	blood
48	chr19:39626200-39628000	Enhancers	Esophagus	oesophagus
49	chr19:39626200-39628200	Enhancers	Pancreas	Pancrea
50	chr19:39626200-39629000	Strong transcription	Fetal Stomach	stomach

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