Variant report

Variant	rs1670546
Chromosome Location	chr11:73585173-73585174
allele	A/T
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	POLR2A	chr11:73584446-73585276	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr11:73584762-73585190	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:73585079-73585531	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:73584983-73586623	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73584965..73587189-chr11:73691735..73694698,2	K562	blood:

Variant related genes	Relation type
PAAF1	TF binding region
ENSG00000175567	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10898948	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10898950	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs11220	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235932	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs1670545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1670558	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3018335	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4362170	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv1038105	chr11:73552023-73673836	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1035977	chr11:73581224-73617653	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1670546	FLJ11848	cis	multi-tissue	Pritchard
rs1670546	PAAF1	cis	Lymphoblastoid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73564400-73586000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr11:73571400-73586000	Weak transcription	Right Atrium	heart
3	chr11:73571600-73586200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:73573000-73586200	Weak transcription	Fetal Brain Male	brain
5	chr11:73575400-73586000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:73576400-73586000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr11:73578000-73586400	Weak transcription	Fetal Heart	heart
8	chr11:73578800-73586200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:73579200-73586400	Weak transcription	Small Intestine	intestine
10	chr11:73579400-73586200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:73579600-73585400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:73579600-73585800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr11:73579600-73585800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:73579600-73586000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:73579600-73586000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:73579600-73586000	Strong transcription	Fetal Thymus	thymus
17	chr11:73579600-73586200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:73579600-73586200	Strong transcription	Fetal Stomach	stomach
19	chr11:73579600-73586200	Strong transcription	Thymus	Thymus
20	chr11:73579800-73586200	Strong transcription	Primary hematopoietic stem cells	blood
21	chr11:73579800-73586200	Strong transcription	Fetal Lung	lung
22	chr11:73580200-73585200	Strong transcription	Brain Cingulate Gyrus	brain
23	chr11:73580200-73585800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr11:73580200-73586200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr11:73580200-73586200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:73580200-73586600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:73580400-73585600	Strong transcription	Dnd41	blood
28	chr11:73580400-73585800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:73580400-73586200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr11:73580400-73586200	Strong transcription	Primary T cells from cord blood	blood
31	chr11:73580400-73586200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:73580400-73586200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr11:73580600-73585800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr11:73580800-73586200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr11:73580800-73586600	Weak transcription	Stomach Mucosa	stomach
36	chr11:73581200-73585200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:73581200-73585800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:73581200-73586000	Strong transcription	A549	lung
39	chr11:73581400-73585200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:73581400-73585600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr11:73581400-73585800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:73581400-73586000	Strong transcription	Fetal Intestine Small	intestine
43	chr11:73581400-73586400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:73581600-73586000	Strong transcription	Liver	Liver
45	chr11:73581600-73586000	Strong transcription	Fetal Intestine Large	intestine
46	chr11:73581600-73586200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:73581600-73586200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr11:73581800-73586200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr11:73582000-73585600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:73582200-73585200	Strong transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links