Variant report

Variant	rs11669124
Chromosome Location	chr19:39623252-39623253
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39340180..39342670-chr19:39622996..39625120,2	MCF-7	breast:
2	chr19:39622898..39624850-chr19:39631546..39633915,2	MCF-7	breast:
3	chr19:39622646..39624803-chr19:39656922..39658959,2	MCF-7	breast:
4	chr19:39618750..39620262-chr19:39623192..39625353,2	K562	blood:
5	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:
6	chr19:39621056..39623320-chr19:39625823..39628576,3	K562	blood:
7	chr19:39620628..39623686-chr19:39793053..39797178,3	K562	blood:
8	chr19:39622591..39626006-chr19:39627126..39631368,3	MCF-7	breast:
9	chr19:39622616..39624773-chr19:39692455..39694487,2	K562	blood:
10	chr19:39621851..39624607-chr19:39667898..39670113,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000269172	Chromatin interaction
ENSG00000130669	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11083508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11666140	0.81[EUR][1000 genomes]
rs11666238	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11671084	0.96[CEU][hapmap]
rs11672886	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][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	0.81[EUR][1000 genomes]
rs12978321	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13228	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs17641276	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs17708461	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304090	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2319152	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35946542	0.81[EUR][1000 genomes]
rs4273158	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4611580	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[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];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803212	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59944493	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs750247	1.00[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs754703	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs754704	0.81[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]
rs874535	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]
rs879689	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11669124	CNFN	cis	cerebellum	SCAN
rs11669124	PAK4	cis	Whole Blood	GTEx
rs11669124	PAK4	cis	Thyroid	GTEx
rs11669124	PAK4	cis	Adipose Subcutaneous	GTEx
rs11669124	B9D2	cis	cerebellum	SCAN
rs11669124	B3GNT8	cis	cerebellum	SCAN
rs11669124	PAK4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:107 , 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	chr19:39617200-39624800	Enhancers	Left Ventricle	heart
4	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:39617600-39625600	Enhancers	Spleen	Spleen
6	chr19:39617600-39627600	Enhancers	Fetal Heart	heart
7	chr19:39617800-39623800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr19:39617800-39624000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:39617800-39624200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr19:39617800-39624600	Enhancers	Stomach Mucosa	stomach
11	chr19:39617800-39625000	Enhancers	Ovary	ovary
12	chr19:39617800-39625200	Enhancers	Pancreas	Pancrea
13	chr19:39617800-39627200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr19:39617800-39628600	Enhancers	Placenta	Placenta
15	chr19:39617800-39630200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
17	chr19:39618000-39623600	Enhancers	Brain Angular Gyrus	brain
18	chr19:39618000-39624400	Enhancers	Liver	Liver
19	chr19:39618000-39624600	Enhancers	Fetal Muscle Leg	muscle
20	chr19:39618200-39623600	Genic enhancers	Fetal Intestine Small	intestine
21	chr19:39618200-39623600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr19:39618200-39628400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr19:39618400-39624600	Enhancers	Fetal Muscle Trunk	muscle
24	chr19:39618400-39626800	Weak transcription	NHEK	skin
25	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr19:39619600-39624400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:39620000-39627200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:39620000-39630000	Weak transcription	HepG2	liver
29	chr19:39620200-39625000	Enhancers	Lung	lung
30	chr19:39620400-39624600	Enhancers	Esophagus	oesophagus
31	chr19:39620400-39624800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:39620600-39626800	Enhancers	Fetal Intestine Large	intestine
33	chr19:39621000-39623400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:39621000-39623400	Genic enhancers	Fetal Stomach	stomach
35	chr19:39621000-39623600	Enhancers	Adipose Nuclei	Adipose
36	chr19:39621000-39623600	Enhancers	Rectal Smooth Muscle	rectum
37	chr19:39621000-39623600	Enhancers	HUVEC	blood vessel
38	chr19:39621000-39623800	Enhancers	Brain Hippocampus Middle	brain
39	chr19:39621000-39624200	Enhancers	Fetal Kidney	kidney
40	chr19:39621000-39624600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:39621000-39624800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr19:39621000-39627200	Enhancers	Fetal Lung	lung
43	chr19:39621000-39628400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:39621200-39624600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:39621400-39624400	Enhancers	Right Ventricle	heart
46	chr19:39621400-39624400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr19:39621400-39624800	Enhancers	Gastric	stomach
48	chr19:39621400-39625200	Enhancers	Duodenum Mucosa	Duodenum
49	chr19:39621400-39628000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr19:39621600-39623400	Enhancers	Right Atrium	heart

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