Variant report

Variant	rs4611580
Chromosome Location	chr19:39621208-39621209
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39205201..39205716-chr19:39621102..39621653,2	MCF-7	breast:
2	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:
3	chr19:39620754..39621927-chr19:39641354..39642257,8	MCF-7	breast:
4	chr19:39601973..39602876-chr19:39620819..39621663,2	MCF-7	breast:
5	chr19:39621056..39623320-chr19:39625823..39628576,3	K562	blood:
6	chr19:39602376..39603706-chr19:39620989..39621663,3	MCF-7	breast:
7	chr19:39620752..39621626-chr19:39634707..39635591,2	MCF-7	breast:
8	chr19:39620628..39623686-chr19:39793053..39797178,3	K562	blood:
9	chr19:39620592..39621547-chr19:39645122..39646030,2	MCF-7	breast:
10	chr12:110684994..110685535-chr19:39620885..39621624,2	MCF-7	breast:
11	chr19:39619517..39621262-chr19:39687570..39690464,2	MCF-7	breast:
12	chr19:39619979..39621693-chr19:39658488..39661418,2	MCF-7	breast:
13	chr19:39620627..39621754-chr19:39641343..39642307,28	MCF-7	breast:
14	chr19:39620732..39621701-chr19:39641353..39642307,11	MCF-7	breast:
15	chr19:39620772..39621728-chr19:39678018..39679083,4	MCF-7	breast:
16	chr19:39620777..39621635-chr19:39899890..39900705,2	MCF-7	breast:
17	chr19:39602746..39603330-chr19:39621049..39621640,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269172	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000188505	Chromatin interaction
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11083508	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11666238	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11669124	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672886	0.82[ASN][1000 genomes]
rs11673014	0.82[ASN][1000 genomes]
rs12327657	0.91[ASN][1000 genomes]
rs12978321	0.86[ASN][1000 genomes]
rs17708461	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2319152	0.82[ASN][1000 genomes]
rs4273158	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803207	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803209	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803212	0.82[ASN][1000 genomes]
rs59944493	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs754703	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs8101281	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs874535	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1067028	chr19:39567228-39622846	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1060469	chr19:39567228-39624790	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	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
6	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4611580	PAK4	cis	Whole Blood	GTEx
rs4611580	PAK4	cis	Skin Sun Exposed Lower leg	GTEx
rs4611580	PAK4	cis	Thyroid	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617000-39622400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:39617000-39630800	Weak transcription	Primary T cells from cord blood	blood
3	chr19:39617000-39635000	Weak transcription	Aorta	Aorta
4	chr19:39617200-39624800	Enhancers	Left Ventricle	heart
5	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr19:39617600-39622000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:39617600-39625600	Enhancers	Spleen	Spleen
8	chr19:39617600-39627600	Enhancers	Fetal Heart	heart
9	chr19:39617800-39622200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:39617800-39622400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr19:39617800-39623000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:39617800-39623200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:39617800-39623800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr19:39617800-39624000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:39617800-39624200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr19:39617800-39624600	Enhancers	Stomach Mucosa	stomach
17	chr19:39617800-39625000	Enhancers	Ovary	ovary
18	chr19:39617800-39625200	Enhancers	Pancreas	Pancrea
19	chr19:39617800-39627200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr19:39617800-39628600	Enhancers	Placenta	Placenta
21	chr19:39617800-39630200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
23	chr19:39618000-39621800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:39618000-39622200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:39618000-39622400	Enhancers	Small Intestine	intestine
26	chr19:39618000-39623600	Enhancers	Brain Angular Gyrus	brain
27	chr19:39618000-39624400	Enhancers	Liver	Liver
28	chr19:39618000-39624600	Enhancers	Fetal Muscle Leg	muscle
29	chr19:39618200-39621600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr19:39618200-39621600	Weak transcription	Fetal Thymus	thymus
31	chr19:39618200-39621800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:39618200-39622000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr19:39618200-39623600	Genic enhancers	Fetal Intestine Small	intestine
34	chr19:39618200-39623600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr19:39618200-39628400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr19:39618400-39621600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:39618400-39621800	Enhancers	Brain Cingulate Gyrus	brain
38	chr19:39618400-39622200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:39618400-39624600	Enhancers	Fetal Muscle Trunk	muscle
40	chr19:39618400-39626800	Weak transcription	NHEK	skin
41	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:39618600-39621600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr19:39618600-39621800	Weak transcription	Fetal Brain Male	brain
44	chr19:39618800-39622200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr19:39619200-39621400	Weak transcription	HMEC	breast
46	chr19:39619400-39621400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr19:39619400-39621400	Weak transcription	Right Ventricle	heart
48	chr19:39619400-39621800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:39619400-39621800	Weak transcription	Fetal Brain Female	brain
50	chr19:39619400-39621800	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links