Variant report

Variant	rs6003539
Chromosome Location	chr22:23519204-23519205
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	EP300	chr22:23519139-23519917	K562	blood:	n/a	n/a
2	CHD2	chr22:23518668-23519977	K562	blood:	n/a	n/a
3	GTF2F1	chr22:23518479-23519988	K562	blood:	n/a	n/a
4	UBTF	chr22:23519128-23519815	K562	blood:	n/a	n/a
5	PML	chr22:23519031-23520086	K562	blood:	n/a	n/a
6	SPI1	chr22:23519109-23519780	K562	blood:	n/a	chr22:23519506-23519515
7	PML	chr22:23518926-23519961	K562	blood:	n/a	n/a
8	GABPA	chr22:23518999-23519793	K562	blood:	n/a	n/a
9	GATA1	chr22:23518698-23519824	K562	blood:	n/a	chr22:23519781-23519797 chr22:23519504-23519521 chr22:23519508-23519518 chr22:23519500-23519510
10	GATA2	chr22:23517735-23520273	K562	blood:	n/a	chr22:23519781-23519797 chr22:23519504-23519521 chr22:23519508-23519518 chr22:23519903-23519916 chr22:23519500-23519510
11	YY1	chr22:23518895-23519208	GM12892	blood:	n/a	n/a
12	SMARCA4	chr22:23518725-23519907	K562	blood:	n/a	n/a
13	TAL1	chr22:23518309-23520017	K562	blood:	n/a	chr22:23519503-23519521
14	TBL1XR1	chr22:23518653-23520012	K562	blood:	n/a	n/a
15	MYC	chr22:23519041-23520050	K562	blood:	n/a	n/a
16	NR2F2	chr22:23518331-23520423	K562	blood:	n/a	n/a
17	TRIM28	chr22:23518168-23519993	K562	blood:	n/a	n/a
18	SETDB1	chr22:23517474-23520050	K562	blood:	n/a	n/a
19	RUNX3	chr22:23518798-23519252	GM12878	blood:	n/a	n/a
20	TBP	chr22:23519014-23519880	K562	blood:	n/a	n/a
21	TEAD4	chr22:23518334-23519977	K562	blood:	n/a	n/a
22	SP2	chr22:23517817-23520428	K562	blood:	n/a	n/a
23	HCFC1	chr22:23518642-23519943	K562	blood:	n/a	n/a
24	GATA2	chr22:23518811-23519836	K562	blood:	n/a	chr22:23519781-23519797 chr22:23519504-23519521 chr22:23519508-23519518 chr22:23519500-23519510
25	JUND	chr22:23519066-23519856	K562	blood:	n/a	n/a
26	MYC	chr22:23519140-23519824	K562	blood:	n/a	n/a
27	SETDB1	chr22:23517855-23519928	K562	blood:	n/a	n/a
28	CBX3	chr22:23517679-23520245	K562	blood:	n/a	n/a
29	CUX1	chr22:23518080-23520088	K562	blood:	n/a	n/a
30	KAP1	chr22:23517822-23519962	K562	blood:	n/a	n/a
31	GABPA	chr22:23518577-23519745	K562	blood:	n/a	n/a
32	MAZ	chr22:23519203-23519765	K562	blood:	n/a	n/a
33	EGR1	chr22:23518552-23519828	K562	blood:	n/a	chr22:23519509-23519518
34	STAT5A	chr22:23517960-23520421	K562	blood:	n/a	chr22:23519509-23519521 chr22:23519764-23519772
35	RCOR1	chr22:23518995-23519968	K562	blood:	n/a	n/a
36	MAFF	chr22:23518710-23519880	K562	blood:	n/a	n/a
37	MAX	chr22:23517931-23520266	K562	blood:	n/a	chr22:23518226-23518235 chr22:23518223-23518232 chr22:23518202-23518212
38	CCNT2	chr22:23519158-23519768	K562	blood:	n/a	n/a
39	ETS1	chr22:23518632-23520442	K562	blood:	n/a	chr22:23519504-23519518 chr22:23519506-23519519 chr22:23519506-23519517 chr22:23519510-23519517
40	NR2F2	chr22:23518315-23522913	K562	blood:	n/a	n/a
41	ZNF274	chr22:23519005-23519926	K562	blood:	n/a	n/a
42	MTA3	chr22:23518792-23519693	GM12878	blood:	n/a	n/a
43	ATF3	chr22:23518587-23520390	K562	blood:	n/a	n/a
44	HMGN3	chr22:23519148-23519796	K562	blood:	n/a	n/a
45	POLR2A	chr22:23518736-23519985	K562	blood:	n/a	n/a
46	RUNX3	chr22:23518372-23519221	GM12878	blood:	n/a	n/a
47	SPI1	chr22:23519148-23519975	K562	blood:	n/a	chr22:23519506-23519515
48	CEBPD	chr22:23518984-23519916	K562	blood:	n/a	n/a
49	MAFK	chr22:23519020-23520014	K562	blood:	n/a	n/a
50	STAT5A	chr22:23518925-23519857	K562	blood:	n/a	chr22:23519509-23519521 chr22:23519764-23519772

No.	Distal block	Cell Line	Cell type
1	chr22:23518770..23520799-chr9:133813002..133814984,2	K562	blood:
2	chr22:23516682..23520309-chr22:23521388..23525029,5	MCF-7	breast:
3	chr22:23518801..23520125-chr22:23623736..23625336,5	K562	blood:
4	chr22:23519177..23520782-chr22:23631685..23633544,2	MCF-7	breast:

Variant related genes	Relation type
BCR	TF binding region
ENSG00000130720	Chromatin interaction
ENSG00000186716	Chromatin interaction
ENSG00000236794	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12157412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12157536	1.00[AMR][1000 genomes]
rs12157941	1.00[AMR][1000 genomes]
rs12158986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12159557	0.92[AFR][1000 genomes]
rs12159793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12160027	1.00[AMR][1000 genomes]
rs12160099	1.00[AMR][1000 genomes]
rs2330366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5996469	1.00[AMR][1000 genomes]
rs5996472	1.00[AMR][1000 genomes]
rs5996477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5996479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5996480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5996481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5996482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5996484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003521	1.00[AMR][1000 genomes]
rs6003522	1.00[AMR][1000 genomes]
rs6003523	1.00[AMR][1000 genomes]
rs6003524	1.00[AMR][1000 genomes]
rs6003526	1.00[AMR][1000 genomes]
rs6003528	1.00[AMR][1000 genomes]
rs6003530	1.00[AMR][1000 genomes]
rs6003537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003540	1.00[AMR][1000 genomes]
rs6003541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003544	1.00[AFR][1000 genomes]
rs6003545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6003628	1.00[AMR][1000 genomes]
rs9620237	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915235	chr22:22971768-23650987	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
2	esv3388845	chr22:22973346-23652447	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	100 gene(s)	inside rSNPs	diseases
3	nsv531799	chr22:22993679-23642142	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
4	nsv1061433	chr22:22997799-23649107	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
5	nsv521695	chr22:22998337-23648009	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
6	nsv915236	chr22:22998337-23650987	Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
7	nsv588512	chr22:22998337-23667731	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv531800	chr22:23002708-23648163	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
9	nsv916593	chr22:23002709-23648790	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
10	nsv993496	chr22:23002709-23654222	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
11	nsv1067002	chr22:23007167-23643363	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
12	nsv1067324	chr22:23007367-23654223	Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
13	nsv533839	chr22:23012013-23643223	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
14	nsv916933	chr22:23012069-23654237	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
15	nsv531801	chr22:23028586-23657804	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	92 gene(s)	inside rSNPs	diseases
16	nsv531802	chr22:23046186-23627391	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	diseases
17	nsv1060509	chr22:23055148-23648719	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	83 gene(s)	inside rSNPs	diseases
18	nsv1056324	chr22:23055148-23750989	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
19	nsv1062780	chr22:23060449-23648719	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
20	nsv948942	chr22:23063178-23645718	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
21	nsv1063200	chr22:23097177-23643224	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	80 gene(s)	inside rSNPs	diseases
22	nsv949250	chr22:23157485-23645718	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
23	nsv1057659	chr22:23400739-24138788	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
24	nsv1058604	chr22:23497533-23545751	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:23490400-23522000	Weak transcription	Aorta	Aorta
2	chr22:23506800-23520600	Weak transcription	Brain Anterior Caudate	brain
3	chr22:23511000-23520800	Weak transcription	Gastric	stomach
4	chr22:23516000-23522000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr22:23516600-23520600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr22:23516600-23520600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr22:23517000-23521000	Weak transcription	Brain Angular Gyrus	brain
8	chr22:23517400-23519600	ZNF genes & repeats	Placenta	Placenta
9	chr22:23517800-23519400	ZNF genes & repeats	K562	blood
10	chr22:23517800-23519600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr22:23517800-23519600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr22:23517800-23519600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
13	chr22:23517800-23519600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
14	chr22:23517800-23519800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr22:23517800-23519800	ZNF genes & repeats	Fetal Thymus	thymus
16	chr22:23517800-23522000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr22:23517800-23522200	Enhancers	GM12878-XiMat	blood
18	chr22:23518000-23519800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr22:23518000-23519800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
20	chr22:23518000-23519800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
21	chr22:23518000-23519800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr22:23518000-23521200	Strong transcription	Right Atrium	heart
23	chr22:23518000-23522000	Enhancers	Esophagus	oesophagus
24	chr22:23518000-23522200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr22:23518200-23520600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr22:23518600-23519400	ZNF genes & repeats	Thymus	Thymus
27	chr22:23518600-23520600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr22:23518800-23519600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr22:23518800-23519800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr22:23518800-23520800	Enhancers	HepG2	liver
31	chr22:23519000-23519600	Enhancers	Pancreas	Pancrea
32	chr22:23519000-23519800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
33	chr22:23519000-23521600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr22:23519200-23519600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr22:23519200-23519800	Enhancers	Duodenum Mucosa	Duodenum
36	chr22:23519200-23521400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr22:23519200-23522200	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links