Variant report

Variant	rs12062897
Chromosome Location	chr1:220537582-220537583
allele	C/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	GATA3	chr1:220535537-220537928	SK-N-SH	brain:	n/a	chr1:220537527-220537536 chr1:220537526-220537536
2	NR2F2	chr1:220537368-220537879	MCF-7	breast:	n/a	chr1:220537581-220537596
3	TCF12	chr1:220536177-220537886	SK-N-SH	brain:	n/a	n/a
4	GATA2	chr1:220536465-220537729	SH-SY5Y	brain:	n/a	chr1:220537527-220537536 chr1:220537526-220537536
5	GATA3	chr1:220536372-220537724	SH-SY5Y	brain:	n/a	chr1:220537527-220537536 chr1:220537526-220537536
6	GATA3	chr1:220536591-220537747	MCF-7	breast:	n/a	chr1:220537527-220537536 chr1:220537526-220537536
7	NR2F2	chr1:220537235-220537867	MCF-7	breast:	n/a	chr1:220537581-220537596
8	SIN3AK20	chr1:220537217-220537978	MCF-7	breast:	n/a	n/a
9	GATA3	chr1:220537369-220537702	MCF-7	breast:	n/a	chr1:220537527-220537536 chr1:220537526-220537536
10	TCF12	chr1:220536273-220537769	SK-N-SH	brain:	n/a	n/a
11	USF1	chr1:220537173-220537596	SK-N-SH	brain:	n/a	n/a
12	EP300	chr1:220535561-220537886	SK-N-SH	brain:	n/a	chr1:220536907-220536916 chr1:220536732-220536741 chr1:220536501-220536511 chr1:220537750-220537764
13	RUNX3	chr1:220537542-220537852	GM12878	blood:	n/a	n/a
14	RUNX3	chr1:220537508-220537948	GM12878	blood:	n/a	n/a
15	GATA3	chr1:220536365-220537965	MCF-7	breast:	n/a	chr1:220537527-220537536 chr1:220537526-220537536
16	ZNF217	chr1:220537401-220537690	MCF-7	breast:	n/a	n/a
17	BATF	chr1:220537571-220537839	GM12878	blood:	n/a	n/a
18	JUND	chr1:220536142-220537755	SK-N-SH	brain:	n/a	chr1:220536731-220536741 chr1:220536731-220536740 chr1:220537242-220537251 chr1:220536732-220536739 chr1:220536730-220536741 chr1:220536732-220536741 chr1:220536730-220536742 chr1:220536731-220536741
19	GATA3	chr1:220536252-220537842	SK-N-SH	brain:	n/a	chr1:220537527-220537536 chr1:220537526-220537536
20	GATA3	chr1:220536472-220537856	MCF-7	breast:	n/a	chr1:220537527-220537536 chr1:220537526-220537536
21	PBX3	chr1:220536255-220537774	SK-N-SH	brain:	n/a	chr1:220537310-220537319

No.	Distal block	Cell Line	Cell type
1	chr1:220509893..220511570-chr1:220536050..220537771,2	MCF-7	breast:
2	chr1:220536671..220538560-chr1:220540237..220541993,2	K562	blood:
3	chr1:220529781..220531415-chr1:220536320..220538470,2	K562	blood:

Variant related genes	Relation type
ENSG00000226927	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11118534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11118535	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12059878	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064931	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12083475	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12090640	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3430143	chr1:220537227-220537679	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220531600-220542200	Weak transcription	Left Ventricle	heart
2	chr1:220536200-220541600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:220536400-220537600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr1:220536600-220537600	Enhancers	Fetal Muscle Leg	muscle
5	chr1:220536600-220537800	Enhancers	Hela-S3	cervix
6	chr1:220536800-220538600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:220536800-220541400	Weak transcription	Osteobl	bone
8	chr1:220536800-220541800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:220537000-220541600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:220537000-220543400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:220537000-220544600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:220537200-220537600	Enhancers	Fetal Heart	heart
13	chr1:220537200-220541400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:220537200-220541600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:220537200-220541600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:220537200-220542200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:220537400-220537600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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