Variant report

Variant	rs12567622
Chromosome Location	chr1:113931145-113931146
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:80)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:80 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:113930777-113931629	SK-N-SH	brain:	n/a	n/a
2	ATF1	chr1:113931046-113931510	K562	blood:	n/a	n/a
3	GATA2	chr1:113930984-113931634	K562	blood:	n/a	n/a
4	SETDB1	chr1:113930275-113931759	U2OS	brain:	n/a	n/a
5	SP1	chr1:113931101-113931775	A549	lung:	n/a	n/a
6	GATA3	chr1:113930809-113931649	MCF-7	breast:	n/a	n/a
7	MYBL2	chr1:113931134-113931705	HepG2	liver:	n/a	n/a
8	KAP1	chr1:113930554-113933084	HEK293	kidney:	n/a	n/a
9	CEBPD	chr1:113931073-113931610	K562	blood:	n/a	n/a
10	POLR2A	chr1:113931091-113931775	SK-N-SH	brain:	n/a	n/a
11	MYBL2	chr1:113931117-113931817	HepG2	liver:	n/a	n/a
12	CTCF	chr1:113931133-113931483	A549	lung:	n/a	n/a
13	STAT5A	chr1:113931068-113931491	K562	blood:	n/a	n/a
14	RAD21	chr1:113931102-113931663	SK-N-SH_RA	brain:	n/a	n/a
15	MAX	chr1:113931107-113931793	A549	lung:	n/a	n/a
16	EP300	chr1:113931130-113931771	A549	lung:	n/a	n/a
17	RAD21	chr1:113931076-113931554	HepG2	liver:	n/a	n/a
18	FOXA2	chr1:113931108-113931804	A549	lung:	n/a	n/a
19	GATA1	chr1:113930839-113931840	PBDE	blood:	n/a	n/a
20	GATA3	chr1:113930714-113931911	SK-N-SH	brain:	n/a	n/a
21	ZNF384	chr1:113931101-113931399	K562	blood:	n/a	n/a
22	EP300	chr1:113930879-113931154	SK-N-SH_RA	brain:	n/a	n/a
23	GATA3	chr1:113930727-113931673	T-47D	breast:	n/a	n/a
24	GATA2	chr1:113930773-113931818	SH-SY5Y	brain:	n/a	n/a
25	TBL1XR1	chr1:113931111-113931453	K562	blood:	n/a	n/a
26	POLR2A	chr1:113931125-113931451	K562	blood:	n/a	n/a
27	ZMIZ1	chr1:113931134-113931451	K562	blood:	n/a	n/a
28	EP300	chr1:113931121-113931831	A549	lung:	n/a	n/a
29	ESR1	chr1:113930766-113931657	T-47D	breast:	n/a	n/a
30	MAX	chr1:113931045-113931817	MCF-7	breast:	n/a	n/a
31	RAD21	chr1:113931070-113931761	SK-N-SH_RA	brain:	n/a	n/a
32	EP300	chr1:113930841-113931709	SK-N-SH_RA	brain:	n/a	n/a
33	EP300	chr1:113931047-113931503	K562	blood:	n/a	n/a
34	RAD21	chr1:113931084-113931603	A549	lung:	n/a	n/a
35	TAL1	chr1:113931025-113931538	K562	blood:	n/a	n/a
36	RAD21	chr1:113931027-113931644	MCF-7	breast:	n/a	n/a
37	NR2F2	chr1:113930853-113931864	MCF-7	breast:	n/a	n/a
38	RCOR1	chr1:113931103-113931796	K562	blood:	n/a	n/a
39	EP300	chr1:113930756-113931227	T-47D	breast:	n/a	n/a
40	GATA3	chr1:113930561-113931686	MCF-7	breast:	n/a	n/a
41	EP300	chr1:113930782-113931679	MCF-7	breast:	n/a	n/a
42	KAP1	chr1:113930717-113932926	U2OS	brain:	n/a	n/a
43	ZNF274	chr1:113930923-113931557	K562	blood:	n/a	n/a
44	JUND	chr1:113930911-113931550	HepG2	liver:	n/a	n/a
45	ESR1	chr1:113930758-113931151	T-47D	breast:	n/a	n/a
46	ZNF217	chr1:113930772-113931741	MCF-7	breast:	n/a	n/a
47	NR2F2	chr1:113931041-113931526	K562	blood:	n/a	n/a
48	SIN3AK20	chr1:113931026-113931905	MCF-7	breast:	n/a	n/a
49	GATA3	chr1:113930757-113931738	T-47D	breast:	n/a	n/a
50	GABPA	chr1:113931091-113931556	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113929860..113932778-chr17:56735135..56736789,2	MCF-7	breast:
2	chr1:113927002..113929717-chr1:113930255..113932026,2	MCF-7	breast:
3	chr1:113912898..113914605-chr1:113928576..113931565,2	MCF-7	breast:
4	chr1:113761704..113762671-chr1:113930964..113931744,2	MCF-7	breast:
5	chr1:113683228..113683839-chr1:113930885..113931565,2	MCF-7	breast:
6	chr1:113749063..113750761-chr1:113929423..113931147,2	MCF-7	breast:
7	chr1:113775818..113778014-chr1:113929925..113932483,2	MCF-7	breast:
8	chr1:113931119..113932828-chr1:113952487..113954122,2	K562	blood:
9	chr1:113820435..113822948-chr1:113930642..113932953,2	MCF-7	breast:
10	chr1:113822173..113823702-chr1:113930402..113933274,2	MCF-7	breast:
11	chr1:113930334..113933089-chr1:114124806..114127254,2	MCF-7	breast:
12	chr1:113683191..113683712-chr1:113930987..113931505,2	MCF-7	breast:
13	chr1:113751160..113752973-chr1:113930438..113931950,2	MCF-7	breast:
14	chr1:113930366..113932771-chr1:114217459..114219362,2	MCF-7	breast:

No data

Variant related genes	Relation type
MAGI3	TF binding region
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10458458	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10458459	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10857994	0.86[ASN][1000 genomes]
rs11102627	0.87[ASN][1000 genomes]
rs11102628	0.87[ASN][1000 genomes]
rs11102630	0.87[ASN][1000 genomes]
rs11102641	0.82[AFR][1000 genomes]
rs11102644	0.82[AFR][1000 genomes]
rs1112085	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1112543	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12021783	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12023641	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12024428	0.93[ASN][1000 genomes]
rs12025806	0.82[AFR][1000 genomes]
rs12029305	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12030900	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12032395	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12034178	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12038879	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12039603	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12045559	0.82[AFR][1000 genomes]
rs12048327	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12049093	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12049447	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12568854	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1418607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1539411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2027536	0.94[ASN][1000 genomes]
rs2027537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2051083	0.82[AFR][1000 genomes]
rs4838987	0.82[AMR][1000 genomes]
rs4839320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55737954	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66565865	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6688827	0.93[ASN][1000 genomes]
rs72687924	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72687938	0.82[AFR][1000 genomes]
rs72687939	0.82[AFR][1000 genomes]
rs72687960	0.82[AFR][1000 genomes]
rs9787276	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113918800-113931200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:113918800-113931200	Weak transcription	Right Atrium	heart
3	chr1:113930800-113931400	Enhancers	Fetal Intestine Small	intestine
4	chr1:113930800-113931600	Enhancers	Fetal Heart	heart
5	chr1:113931000-113931200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr1:113931000-113931200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:113931000-113931200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:113931000-113931200	Enhancers	Fetal Intestine Large	intestine
9	chr1:113931000-113931200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr1:113931000-113931200	Enhancers	HMEC	breast
11	chr1:113931000-113931200	Enhancers	NHEK	skin
12	chr1:113931000-113931200	Enhancers	NHLF	lung
13	chr1:113931000-113931200	Enhancers	Osteobl	bone
14	chr1:113931000-113931400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:113931000-113931400	Flanking Active TSS	A549	lung
16	chr1:113931000-113931400	Flanking Active TSS	HepG2	liver
17	chr1:113931000-113931600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
18	chr1:113931000-113931800	Enhancers	Fetal Kidney	kidney
19	chr1:113931000-113932000	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links