Variant report

Variant	rs1009730
Chromosome Location	chr22:34260738-34260739
allele	A/G
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	EBF1	chr22:34260631-34260875	GM12878	blood:	n/a	chr22:34260744-34260755
2	RCOR1	chr22:34260581-34260855	HepG2	liver:	n/a	n/a
3	CEBPB	chr22:34260638-34261057	HepG2	liver:	n/a	chr22:34260820-34260831
4	NR2F2	chr22:34260649-34261694	MCF-7	breast:	n/a	n/a
5	CEBPB	chr22:34260670-34260959	HepG2	liver:	n/a	chr22:34260820-34260831
6	MTA3	chr22:34260557-34261183	GM12878	blood:	n/a	n/a
7	MTA3	chr22:34260426-34261105	GM12878	blood:	n/a	n/a
8	CEBPB	chr22:34260593-34260981	HepG2	liver:	n/a	chr22:34260820-34260831
9	MYC	chr22:34260636-34260915	NB4	blood:	n/a	n/a
10	SRF	chr22:34260706-34260965	HepG2	liver:	n/a	chr22:34260834-34260851 chr22:34260835-34260850 chr22:34260834-34260852
11	ARID3A	chr22:34260707-34261720	HepG2	liver:	n/a	n/a
12	CEBPB	chr22:34260638-34261015	IMR90	lung:	n/a	chr22:34260820-34260831
13	CEBPB	chr22:34260708-34260897	A549	lung:	n/a	chr22:34260820-34260831
14	HDAC2	chr22:34260671-34260982	HepG2	liver:	n/a	n/a
15	RXRA	chr22:34260703-34261050	HepG2	liver:	n/a	chr22:34260919-34260932 chr22:34260771-34260780 chr22:34260919-34260932 chr22:34260915-34260935 chr22:34260919-34260933 chr22:34260919-34260932
16	CEBPB	chr22:34260696-34261005	MCF-7	breast:	n/a	chr22:34260820-34260831
17	USF2	chr22:34260531-34260763	GM12878	blood:	n/a	n/a
18	NFIC	chr22:34260661-34261065	GM12878	blood:	n/a	n/a
19	RUNX3	chr22:34260515-34261105	GM12878	blood:	n/a	n/a
20	SRF	chr22:34260687-34260985	HepG2	liver:	n/a	chr22:34260834-34260851 chr22:34260835-34260850 chr22:34260834-34260852
21	EBF1	chr22:34260664-34260896	GM12878	blood:	n/a	chr22:34260744-34260755
22	CEBPB	chr22:34260635-34261548	HepG2	liver:	n/a	chr22:34260820-34260831
23	SPI1	chr22:34260681-34260903	GM12891	blood:	n/a	n/a
24	RUNX3	chr22:34260514-34261110	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:34259639..34261419-chr22:34267116..34269181,2	MCF-7	breast:
2	chr22:34248614..34251924-chr22:34259957..34262591,3	MCF-7	breast:
3	chr22:34260736..34263686-chr22:34313890..34318281,7	MCF-7	breast:

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

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13056358	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13057617	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13058568	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1547409	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]
rs1807710	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2018292	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2267306	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs34780334	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35709129	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs496956	1.00[CHB][hapmap]
rs8138735	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607079	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs9607080	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9607086	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9609876	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9609877	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9609878	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9609879	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9609881	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9609882	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9609883	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv524156	chr22:34145596-34260738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1009730	LARGE	cis	cerebellum	SCAN
rs1009730	KREMEN1	cis	cerebellum	SCAN

Chromatin state (count:60 , 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	chr22:34250000-34261000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr22:34250800-34261000	Weak transcription	Fetal Brain Male	brain
4	chr22:34251000-34269200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr22:34251200-34268000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr22:34252400-34267600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr22:34254400-34268000	Weak transcription	Spleen	Spleen
8	chr22:34254600-34269200	Weak transcription	Fetal Stomach	stomach
9	chr22:34255800-34261000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr22:34256200-34269600	Enhancers	Fetal Heart	heart
11	chr22:34256400-34267000	Enhancers	Left Ventricle	heart
12	chr22:34257200-34260800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr22:34257200-34269200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr22:34257200-34269600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr22:34257400-34264400	Weak transcription	Brain Hippocampus Middle	brain
16	chr22:34257600-34260800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr22:34257600-34260800	Weak transcription	Brain Angular Gyrus	brain
18	chr22:34257600-34260800	Weak transcription	Brain Anterior Caudate	brain
19	chr22:34257600-34261000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr22:34257600-34264400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr22:34257600-34265600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr22:34257600-34265600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr22:34257600-34269600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr22:34257800-34260800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr22:34257800-34261000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr22:34258600-34263400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr22:34259200-34261800	Enhancers	Stomach Mucosa	stomach
28	chr22:34259600-34263600	Enhancers	Fetal Intestine Large	intestine
29	chr22:34259800-34260800	Enhancers	Right Ventricle	heart
30	chr22:34259800-34261400	Enhancers	Ovary	ovary
31	chr22:34260000-34261600	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr22:34260000-34261600	Enhancers	Fetal Intestine Small	intestine
33	chr22:34260000-34261800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr22:34260000-34261800	Enhancers	Liver	Liver
35	chr22:34260000-34261800	Enhancers	Right Atrium	heart
36	chr22:34260000-34262800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr22:34260200-34261600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr22:34260200-34269000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr22:34260400-34261200	Enhancers	Brain Substantia Nigra	brain
40	chr22:34260400-34261200	Enhancers	Colonic Mucosa	Colon
41	chr22:34260400-34261200	Enhancers	Gastric	stomach
42	chr22:34260400-34261200	Flanking Active TSS	GM12878-XiMat	blood
43	chr22:34260400-34261400	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr22:34260400-34261600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr22:34260400-34261600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr22:34260400-34261600	Enhancers	Adipose Nuclei	Adipose
47	chr22:34260400-34261600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr22:34260400-34261600	Enhancers	HSMMtube	muscle
49	chr22:34260400-34261800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr22:34260400-34264600	Enhancers	Rectal Mucosa Donor 31	rectum

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