Variant report

Variant	rs7772682
Chromosome Location	chr6:28695668-28695669
allele	A/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	IRF1	chr6:28694816-28696122	K562	blood:	n/a	chr6:28694954-28694968 chr6:28695568-28695579 chr6:28694950-28694964 chr6:28695259-28695273 chr6:28695566-28695580 chr6:28695567-28695578 chr6:28694952-28694972 chr6:28695565-28695579 chr6:28694992-28695004 chr6:28695567-28695581 chr6:28695565-28695585 chr6:28694954-28694964
2	ARID3A	chr6:28693225-28696326	K562	blood:	n/a	chr6:28693710-28693726
3	SPI1	chr6:28695272-28695851	GM12878	blood:	n/a	chr6:28695567-28695576
4	SPI1	chr6:28695379-28695740	GM12878	blood:	n/a	chr6:28695567-28695576
5	SPI1	chr6:28695374-28695721	GM12891	blood:	n/a	chr6:28695567-28695576
6	SPI1	chr6:28695326-28695714	GM12891	blood:	n/a	chr6:28695567-28695576
7	TEAD4	chr6:28694604-28696040	K562	blood:	n/a	n/a
8	STAT2	chr6:28695348-28695972	K562	blood:	n/a	chr6:28695567-28695578 chr6:28695565-28695580
9	POLR2A	chr6:28695609-28695683	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28695149..28697621-chr6:28743260..28745137,3	K562	blood:
2	chr6:28694596..28696864-chr6:28727942..28730829,2	K562	blood:
3	chr6:28693274..28695982-chr6:28860211..28863205,2	K562	blood:
4	chr6:28694465..28699409-chr6:28701823..28706376,12	K562	blood:
5	chr6:28694415..28696951-chr6:28906885..28909854,2	K562	blood:
6	chr6:28695047..28697144-chr6:28756622..28759292,2	K562	blood:
7	chr6:28649222..28651616-chr6:28694274..28696265,2	MCF-7	breast:
8	chr6:28694600..28696603-chr6:28717973..28720482,2	K562	blood:
9	chr6:28666298..28671313-chr6:28695437..28699521,5	K562	blood:
10	chr6:28694799..28697435-chr6:28950609..28952532,2	K562	blood:
11	chr6:28695559..28699343-chr6:28721391..28727067,6	K562	blood:
12	chr6:28693769..28696400-chr6:28804513..28806706,3	K562	blood:
13	chr6:27859745..27862203-chr6:28694070..28696885,3	K562	blood:
14	chr6:28695552..28697065-chr6:28863469..28865402,2	K562	blood:
15	chr6:28693500..28696718-chr6:28743195..28744760,3	K562	blood:
16	chr6:28690825..28693776-chr6:28694018..28695886,2	MCF-7	breast:
17	chr6:28695145..28698066-chr6:28723238..28727067,5	K562	blood:
18	chr6:28693622..28696352-chr6:28828631..28830226,2	K562	blood:
19	chr6:28693863..28696096-chr6:28729329..28732311,2	K562	blood:

Variant related genes	Relation type
RPSAP2	TF binding region
ENSG00000221191	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000213916	Chromatin interaction
ENSG00000224157	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10498733	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1107160	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1233582	0.88[ASN][1000 genomes]
rs17280797	0.97[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17280818	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17281186	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17346574	0.84[ASN][1000 genomes]
rs1891757	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1936180	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3999045	0.90[AMR][1000 genomes]
rs55641015	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55659253	0.95[AMR][1000 genomes]
rs55764335	0.95[AMR][1000 genomes]
rs55891766	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56003969	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs56098960	0.95[AMR][1000 genomes]
rs56165011	0.95[AMR][1000 genomes]
rs56296645	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56384403	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57170714	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57693980	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57748269	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs57791058	0.95[AMR][1000 genomes]
rs57965355	0.95[AMR][1000 genomes]
rs58104924	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs58238888	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58258185	0.95[AMR][1000 genomes]
rs59233561	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs59475656	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs59959723	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs60252686	0.95[AMR][1000 genomes]
rs60311527	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61094745	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs61208746	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61657599	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61703239	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6901325	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6905871	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6906105	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6906506	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6909960	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6916286	0.91[AMR][1000 genomes]
rs6923795	0.95[AMR][1000 genomes]
rs7738101	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7742889	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7748319	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7751451	0.95[AMR][1000 genomes]
rs7751884	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7754365	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7755641	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7758798	0.95[AMR][1000 genomes]
rs7760656	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7765829	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7766599	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7772111	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772373	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7772482	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9688414	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9767343	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9767359	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7772682	ZNF323	cis	cerebellum	SCAN
rs7772682	ZSCAN23	cis	cerebellum	SCAN
rs7772682	FAM65B	cis	cerebellum	SCAN
rs7772682	ZKSCAN3	cis	cerebellum	SCAN
rs7772682	ZNF323	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28693600-28696200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:28693800-28696200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:28694200-28697800	Active TSS	K562	blood
4	chr6:28695400-28695800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:28695400-28695800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:28695400-28696200	Bivalent Enhancer	HepG2	liver
7	chr6:28695600-28695800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
8	chr6:28695600-28695800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:28695600-28696000	Flanking Active TSS	Hela-S3	cervix
10	chr6:28695600-28696000	Flanking Active TSS	HMEC	breast
11	chr6:28695600-28696200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:28695600-28696200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:28695600-28696200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:28695600-28696200	Flanking Active TSS	A549	lung
15	chr6:28695600-28696200	Enhancers	GM12878-XiMat	blood

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