Variant report

Variant	rs28565871
Chromosome Location	chr4:97273400-97273401
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	RAD21	chr4:97273274-97273821	MCF-7	breast:	n/a	n/a
2	GATA2	chr4:97273186-97273522	HUVEC	blood vessel:	n/a	chr4:97273363-97273379
3	MAFK	chr4:97273124-97273701	H1-hESC	embryonic stem cell:	n/a	chr4:97273297-97273308 chr4:97273302-97273312 chr4:97273302-97273311 chr4:97273297-97273312
4	MAFK	chr4:97273144-97273546	K562	blood:	n/a	chr4:97273297-97273308 chr4:97273302-97273312 chr4:97273302-97273311 chr4:97273297-97273312
5	RAD21	chr4:97273252-97273865	HCT-116	colon:	n/a	n/a
6	RAD21	chr4:97273165-97273734	ECC-1	luminal epithelium:	n/a	n/a
7	MAFF	chr4:97273154-97273464	K562	blood:	n/a	chr4:97273295-97273313
8	CTCF	chr4:97273391-97273702	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr4:97273388-97273823	MCF-7	breast:	n/a	n/a
10	CTCF	chr4:97273397-97273677	SK-N-SH_RA	brain:	n/a	n/a
11	RAD21	chr4:97273359-97273757	GM12878	blood:	n/a	n/a
12	RAD21	chr4:97273014-97273961	SK-N-SH	brain:	n/a	n/a
13	ZNF384	chr4:97273387-97273672	GM12878	blood:	n/a	n/a
14	MAFK	chr4:97272870-97273482	HepG2	liver:	n/a	chr4:97273297-97273308 chr4:97273302-97273312 chr4:97273302-97273311 chr4:97273297-97273312
15	SMC3	chr4:97273307-97273761	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr4:97273310-97273663	H1-hESC	embryonic stem cell:	n/a	chr4:97273500-97273513 chr4:97273500-97273513 chr4:97273502-97273513 chr4:97273502-97273513
17	JUND	chr4:97273287-97273666	H1-hESC	embryonic stem cell:	n/a	chr4:97273515-97273524 chr4:97273303-97273313
18	ZKSCAN1	chr4:97273400-97273734	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr4:97273380-97273530	MCF-7	breast:	n/a	n/a
20	MAFK	chr4:97273148-97273475	HepG2	liver:	n/a	chr4:97273297-97273308 chr4:97273302-97273312 chr4:97273302-97273311 chr4:97273297-97273312
21	MAFF	chr4:97273138-97273487	HepG2	liver:	n/a	chr4:97273295-97273313
22	RAD21	chr4:97273108-97273839	H1-hESC	embryonic stem cell:	n/a	n/a
23	RAD21	chr4:97273330-97273752	SK-N-SH_RA	brain:	n/a	n/a
24	E2F4	chr4:97273342-97273850	MCF10A-Er-Src	breast:	n/a	n/a
25	RAD21	chr4:97273397-97273693	A549	lung:	n/a	n/a
26	RAD21	chr4:97273361-97273781	SK-N-SH_RA	brain:	n/a	n/a
27	RAD21	chr4:97273200-97273859	MCF-7	breast:	n/a	n/a
28	CEBPB	chr4:97273282-97273661	HCT-116	colon:	n/a	chr4:97273500-97273513 chr4:97273500-97273513 chr4:97273502-97273513 chr4:97273502-97273513
29	RAD21	chr4:97273384-97273700	HepG2	liver:	n/a	n/a
30	RAD21	chr4:97273373-97273755	A549	lung:	n/a	n/a
31	RAD21	chr4:97273325-97273738	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAFK	chr4:97273155-97273454	IMR90	lung:	n/a	chr4:97273297-97273308 chr4:97273302-97273312 chr4:97273302-97273311 chr4:97273297-97273312
33	CTCF	chr4:97273066-97273787	SK-N-SH	brain:	n/a	n/a
34	RAD21	chr4:97273286-97273778	Hela-S3	cervix:	n/a	n/a
35	SETDB1	chr4:97273239-97273834	U2OS	brain:	n/a	n/a
36	POLR2A	chr4:97273309-97273505	MCF10A-Er-Src	breast:	n/a	n/a
37	SMC3	chr4:97273102-97273971	SK-N-SH	brain:	n/a	n/a
38	ZNF384	chr4:97273312-97273655	K562	blood:	n/a	n/a
39	CTCF	chr4:97273322-97273799	MCF-7	breast:	n/a	n/a
40	BACH1	chr4:97273134-97273675	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr4:97273274-97273825	HCT-116	colon:	n/a	n/a
42	MAFK	chr4:97273232-97273470	Hela-S3	cervix:	n/a	chr4:97273297-97273308 chr4:97273302-97273312 chr4:97273302-97273311 chr4:97273297-97273312
43	RAD21	chr4:97273128-97273776	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr4:97273322-97273713	ECC-1	luminal epithelium:	n/a	n/a
45	RAD21	chr4:97273174-97273921	HCT-116	colon:	n/a	n/a
46	CTCF	chr4:97273373-97273795	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:97003956..97004522-chr4:97272708..97273630,2	MCF-7	breast:
2	chr4:96557966..96558741-chr4:97273098..97274003,3	MCF-7	breast:
3	chr4:96614781..96615424-chr4:97273090..97273698,2	MCF-7	breast:

Variant related genes	Relation type
RN7SKP28	TF binding region

Extended variants
information (count: 132 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10002816	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10004804	0.86[EUR][1000 genomes]
rs10006557	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10007900	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10015613	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10021889	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10213429	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10856919	0.86[EUR][1000 genomes]
rs11097501	0.88[ASN][1000 genomes]
rs11097502	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11097505	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11932384	0.83[ASN][1000 genomes]
rs11935830	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12499067	0.81[ASN][1000 genomes]
rs12501360	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12508802	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12509883	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12642471	0.85[ASN][1000 genomes]
rs12644982	0.83[ASN][1000 genomes]
rs12650441	0.92[ASN][1000 genomes]
rs13102896	0.84[ASN][1000 genomes]
rs13104802	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13121458	0.88[ASN][1000 genomes]
rs13122821	0.88[ASN][1000 genomes]
rs13122856	0.89[ASN][1000 genomes]
rs13150508	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354704	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1354706	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1373331	0.83[ASN][1000 genomes]
rs1395199	0.92[ASN][1000 genomes]
rs1425361	0.80[ASN][1000 genomes]
rs1444021	0.88[ASN][1000 genomes]
rs1506304	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506305	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1506306	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506317	0.91[ASN][1000 genomes]
rs1506318	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1506319	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506320	0.93[ASN][1000 genomes]
rs1506321	0.87[ASN][1000 genomes]
rs1567036	0.92[ASN][1000 genomes]
rs1605227	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17025493	0.89[ASN][1000 genomes]
rs1834360	0.80[ASN][1000 genomes]
rs1847963	0.92[ASN][1000 genomes]
rs1847964	0.88[ASN][1000 genomes]
rs1847966	0.83[ASN][1000 genomes]
rs1847967	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1847968	0.88[ASN][1000 genomes]
rs1847969	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1857889	0.92[ASN][1000 genomes]
rs1857890	0.85[ASN][1000 genomes]
rs1867400	0.88[ASN][1000 genomes]
rs1911074	0.93[ASN][1000 genomes]
rs1911076	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1911077	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1948912	0.91[ASN][1000 genomes]
rs2048022	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2083922	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2113973	0.83[ASN][1000 genomes]
rs2174584	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2197322	0.91[ASN][1000 genomes]
rs28407945	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28523416	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28633781	0.92[ASN][1000 genomes]
rs2865736	0.93[ASN][1000 genomes]
rs28788633	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35257138	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36039803	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4146410	0.91[ASN][1000 genomes]
rs4146411	0.91[ASN][1000 genomes]
rs4343731	0.85[ASN][1000 genomes]
rs4414959	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4611939	0.93[ASN][1000 genomes]
rs4613576	0.93[ASN][1000 genomes]
rs4619895	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699283	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699285	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699287	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699288	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4699485	0.81[ASN][1000 genomes]
rs4699496	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4699501	0.93[ASN][1000 genomes]
rs4699503	0.89[ASN][1000 genomes]
rs4699512	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4699513	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs5017329	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55680326	0.87[ASN][1000 genomes]
rs58334182	0.84[ASN][1000 genomes]
rs60275360	0.85[ASN][1000 genomes]
rs6532596	0.81[ASN][1000 genomes]
rs6532597	0.81[ASN][1000 genomes]
rs6532600	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6815558	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6815743	0.91[ASN][1000 genomes]
rs6816447	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820075	0.85[ASN][1000 genomes]
rs6826156	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6826817	0.80[ASN][1000 genomes]
rs6830120	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6832934	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835808	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6837318	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6841294	0.93[ASN][1000 genomes]
rs6855768	0.92[ASN][1000 genomes]
rs6857113	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72883800	0.91[ASN][1000 genomes]
rs72885446	0.89[ASN][1000 genomes]
rs72885485	0.82[ASN][1000 genomes]
rs7653937	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs766061	0.92[ASN][1000 genomes]
rs7671604	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7673756	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7676317	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7676764	0.81[ASN][1000 genomes]
rs7686174	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7690397	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9307167	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9307168	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs931841	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931842	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938547	0.83[ASN][1000 genomes]
rs938548	0.83[ASN][1000 genomes]
rs9686051	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9884259	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9884940	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9998383	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999006	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[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	nsv470057	chr4:97104880-97311657	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv461589	chr4:97104881-97311657	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv594916	chr4:97104881-97311657	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv879632	chr4:97118539-97308914	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:97272800-97274000	Enhancers	HUVEC	blood vessel
2	chr4:97273000-97273600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr4:97273000-97273600	Enhancers	Dnd41	blood
4	chr4:97273000-97274000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr4:97273200-97273400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:97273200-97273400	Enhancers	Fetal Intestine Small	intestine
7	chr4:97273200-97273400	Enhancers	Stomach Mucosa	stomach
8	chr4:97273200-97273600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr4:97273200-97273600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr4:97273200-97273600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr4:97273200-97273800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:97273200-97274000	Enhancers	Primary hematopoietic stem cells	blood
13	chr4:97273400-97275000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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