Variant report

Variant	rs1547409
Chromosome Location	chr22:34261643-34261644
allele	A/C
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	NR2F2	chr22:34260649-34261694	MCF-7	breast:	n/a	n/a
2	ARID3A	chr22:34260707-34261720	HepG2	liver:	n/a	n/a
3	FOSL2	chr22:34261228-34261645	HepG2	liver:	n/a	chr22:34261443-34261454 chr22:34261443-34261453 chr22:34261445-34261452 chr22:34261444-34261453 chr22:34261444-34261452

No.	Distal block	Cell Line	Cell type
1	chr22:34261283..34264105-chr22:34285527..34288136,2	MCF-7	breast:
2	chr22:34248614..34251924-chr22:34259957..34262591,3	MCF-7	breast:
3	chr22:34247996..34248570-chr22:34261032..34261815,2	MCF-7	breast:
4	chr22:34248231..34249994-chr22:34261049..34263874,2	MCF-7	breast:
5	chr22:34261522..34263199-chr22:34316447..34319258,2	MCF-7	breast:
6	chr22:34255181..34259842-chr22:34260995..34265736,9	MCF-7	breast:
7	chr22:34260736..34263686-chr22:34313890..34318281,7	MCF-7	breast:

Variant related genes	Relation type
LARGE	TF binding region
ENSG00000273082	Chromatin interaction
ENSG00000133424	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1009730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13056358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13057617	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13058568	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1807710	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2018292	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34780334	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35709129	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs496956	1.00[CHB][hapmap]
rs8138735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607079	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9607080	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9607086	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9609876	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9609877	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9609878	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9609879	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9609881	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9609882	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9609883	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv914991	chr22:34106384-34293516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1056553	chr22:34116979-34286191	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv914992	chr22:34135007-34283144	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1061736	chr22:34178034-34394918	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv544689	chr22:34178034-34394918	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1066419	chr22:34231732-34553006	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv544690	chr22:34231732-34553006	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv3343210	chr22:34236744-34404210	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34247800-34263000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr22:34251000-34269200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr22:34251200-34268000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:34252400-34267600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr22:34254400-34268000	Weak transcription	Spleen	Spleen
6	chr22:34254600-34269200	Weak transcription	Fetal Stomach	stomach
7	chr22:34256200-34269600	Enhancers	Fetal Heart	heart
8	chr22:34256400-34267000	Enhancers	Left Ventricle	heart
9	chr22:34257200-34269200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr22:34257200-34269600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr22:34257400-34264400	Weak transcription	Brain Hippocampus Middle	brain
12	chr22:34257600-34264400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr22:34257600-34265600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr22:34257600-34265600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr22:34257600-34269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr22:34258600-34263400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr22:34259200-34261800	Enhancers	Stomach Mucosa	stomach
18	chr22:34259600-34263600	Enhancers	Fetal Intestine Large	intestine
19	chr22:34260000-34261800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr22:34260000-34261800	Enhancers	Liver	Liver
21	chr22:34260000-34261800	Enhancers	Right Atrium	heart
22	chr22:34260000-34262800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr22:34260200-34269000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr22:34260400-34261800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr22:34260400-34264600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr22:34260400-34264600	Enhancers	NHLF	lung
27	chr22:34260400-34266400	Enhancers	Rectal Smooth Muscle	rectum
28	chr22:34260400-34266800	Enhancers	Psoas Muscle	Psoas
29	chr22:34260600-34261800	Flanking Active TSS	HepG2	liver
30	chr22:34260800-34262400	Weak transcription	Right Ventricle	heart
31	chr22:34261000-34261800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr22:34261000-34262600	Weak transcription	Small Intestine	intestine
33	chr22:34261000-34263600	Weak transcription	Aorta	Aorta
34	chr22:34261000-34264600	Enhancers	Fetal Brain Male	brain
35	chr22:34261000-34268000	Weak transcription	Pancreas	Pancrea
36	chr22:34261200-34262400	Weak transcription	Colonic Mucosa	Colon
37	chr22:34261200-34262400	Weak transcription	Gastric	stomach
38	chr22:34261200-34263000	Weak transcription	Lung	lung
39	chr22:34261200-34263800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr22:34261200-34264800	Weak transcription	Brain Substantia Nigra	brain
41	chr22:34261200-34268200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr22:34261200-34269400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr22:34261400-34261800	Enhancers	Stomach Smooth Muscle	stomach
44	chr22:34261400-34262400	Weak transcription	NHDF-Ad	bronchial
45	chr22:34261400-34263000	Weak transcription	Ovary	ovary
46	chr22:34261400-34263000	Weak transcription	Osteobl	bone
47	chr22:34261400-34263600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr22:34261600-34262000	Weak transcription	Fetal Intestine Small	intestine
49	chr22:34261600-34262200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr22:34261600-34262200	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links