Variant report

Variant	rs11880094
Chromosome Location	chr19:40325640-40325641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr19:40324038-40325677	A549	lung:	n/a	n/a
2	POLR2A	chr19:40323486-40325688	GM12878	blood:	n/a	n/a
3	SIN3AK20	chr19:40319989-40326136	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:40306432-40338982	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:40322919-40325645	SK-N-MC	brain:	n/a	n/a
6	MXI1	chr19:40323390-40325752	SK-N-SH	brain:	n/a	chr19:40324858-40324867
7	SIX5	chr19:40323974-40325785	A549	lung:	n/a	n/a
8	POLR2A	chr19:40324108-40325756	K562	blood:	n/a	n/a
9	EP300	chr19:40323113-40325687	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr19:40324846-40326381	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:40324148-40325706	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40323585..40327109-chr19:40328017..40332842,7	MCF-7	breast:
2	chr19:40318662..40321360-chr19:40322185..40325984,6	MCF-7	breast:
3	chr19:40324934..40327706-chr19:40474760..40476442,2	K562	blood:
4	chr19:40323873..40328898-chr19:40330848..40333267,4	MCF-7	breast:
5	chr19:39926032..39928483-chr19:40324303..40326455,2	MCF-7	breast:
6	chr19:40321340..40326326-chr19:40333108..40338214,12	MCF-7	breast:
7	chr19:39900130..39902222-chr19:40323529..40326104,2	MCF-7	breast:
8	chr19:40323895..40326074-chr19:40326895..40329517,2	MCF-7	breast:

No data

Variant related genes	Relation type
DYRK1B	TF binding region
ENSG00000105204	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000105202	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10422280	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11880956	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11883249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12459589	0.81[GIH][hapmap]
rs12975624	0.86[CHB][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap]
rs12980289	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12986299	0.84[CHB][hapmap]
rs2072290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2354471	0.81[GIH][hapmap]
rs2354800	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3810383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3810386	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs616650	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs619350	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62106867	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508912	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508913	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs718066	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246501	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7247063	0.81[GIH][hapmap]
rs7248926	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7250408	0.82[GIH][hapmap]
rs7253739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7254914	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258351	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11880094	B9D2	cis	cerebellum	SCAN
rs11880094	ERF	cis	parietal	SCAN
rs11880094	PHLDB3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40318000-40331800	Strong transcription	HepG2	liver
2	chr19:40324800-40327000	Weak transcription	Aorta	Aorta
3	chr19:40324800-40327000	Weak transcription	Ovary	ovary
4	chr19:40324800-40327000	Weak transcription	Small Intestine	intestine
5	chr19:40324800-40327200	Weak transcription	Psoas Muscle	Psoas
6	chr19:40324800-40327400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:40324800-40336000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:40325000-40325800	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
9	chr19:40325000-40325800	Transcr. at gene 5' and 3'	Fetal Lung	lung
10	chr19:40325200-40325800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr19:40325200-40330400	Strong transcription	HSMMtube	muscle
12	chr19:40325200-40330400	Strong transcription	NH-A	brain
13	chr19:40325200-40330600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:40325200-40331800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:40325200-40331800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:40325200-40332200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:40325200-40332600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:40325200-40332600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr19:40325200-40333000	Weak transcription	Right Atrium	heart
20	chr19:40325400-40325800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:40325400-40325800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:40325400-40325800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:40325400-40325800	Strong transcription	Primary T cells from cord blood	blood
24	chr19:40325400-40325800	Strong transcription	Colonic Mucosa	Colon
25	chr19:40325400-40325800	Genic enhancers	Fetal Intestine Small	intestine
26	chr19:40325400-40325800	Strong transcription	Right Ventricle	heart
27	chr19:40325400-40326000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:40325400-40326000	Genic enhancers	Fetal Muscle Leg	muscle
29	chr19:40325400-40326200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:40325400-40326200	Weak transcription	Thymus	Thymus
31	chr19:40325400-40326200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr19:40325400-40326400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr19:40325400-40326600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr19:40325400-40326800	Weak transcription	Brain Substantia Nigra	brain
35	chr19:40325400-40327000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:40325400-40327000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:40325400-40327000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:40325400-40327000	Weak transcription	Colon Smooth Muscle	Colon
39	chr19:40325400-40327000	Weak transcription	Gastric	stomach
40	chr19:40325400-40327000	Weak transcription	Left Ventricle	heart
41	chr19:40325400-40327000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:40325400-40327600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:40325400-40329000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:40325400-40329000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:40325400-40329400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:40325400-40329600	Strong transcription	Esophagus	oesophagus
47	chr19:40325400-40330400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:40325400-40330400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:40325400-40330400	Strong transcription	HSMM	muscle
50	chr19:40325400-40330600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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