Variant report

Variant	rs6959347
Chromosome Location	chr7:55862375-55862376
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	CEBPB	chr7:55862234-55862519	K562	blood:	n/a	chr7:55862399-55862410
2	JUND	chr7:55862315-55862516	HepG2	liver:	n/a	chr7:55862363-55862374
3	MYC	chr7:55862243-55862553	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr7:55862324-55862524	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr7:55862286-55862561	HepG2	liver:	n/a	chr7:55862399-55862410
6	FOSL2	chr7:55862261-55862503	MCF-7	breast:	n/a	chr7:55862362-55862373
7	JUN	chr7:55862191-55862538	Hela-S3	cervix:	n/a	n/a
8	MYC	chr7:55862312-55862554	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr7:55862154-55862607	MCF10A-Er-Src	breast:	n/a	n/a
10	JUND	chr7:55862255-55862574	HCT-116	colon:	n/a	chr7:55862363-55862374
11	RCOR1	chr7:55862303-55862513	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr7:55862330-55862502	Hela-S3	cervix:	n/a	n/a
13	FOSL1	chr7:55862268-55862665	HCT-116	colon:	n/a	n/a
14	MAFK	chr7:55862297-55862546	Hela-S3	cervix:	n/a	n/a
15	STAT3	chr7:55862297-55862620	MCF10A-Er-Src	breast:	n/a	n/a
16	EP300	chr7:55862298-55862507	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr7:55862360-55862510	SAEC	small airway:	n/a	n/a
18	POLR2A	chr7:55862241-55862430	HCT-116	colon:	n/a	n/a
19	FOSL1	chr7:55862233-55862566	HCT-116	colon:	n/a	n/a
20	ZKSCAN1	chr7:55862326-55862393	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr7:55862340-55862490	SAEC	small airway:	n/a	n/a
22	FOSL2	chr7:55862262-55862557	HepG2	liver:	n/a	chr7:55862362-55862373
23	CEBPB	chr7:55862243-55862570	Hela-S3	cervix:	n/a	chr7:55862399-55862410
24	STAT3	chr7:55862288-55862568	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr7:55862187-55862560	MCF10A-Er-Src	breast:	n/a	n/a
26	CEBPB	chr7:55862268-55862679	HCT-116	colon:	n/a	chr7:55862399-55862410
27	CTCF	chr7:55862260-55862410	HMEC	breast:	n/a	n/a
28	JUND	chr7:55862292-55862508	HepG2	liver:	n/a	chr7:55862363-55862374
29	MAFK	chr7:55862299-55862520	HepG2	liver:	n/a	n/a
30	CEBPB	chr7:55862294-55862497	HepG2	liver:	n/a	chr7:55862399-55862410
31	CTCF	chr7:55862360-55862510	HepG2	liver:	n/a	n/a
32	CHD2	chr7:55862308-55862515	Hela-S3	cervix:	n/a	n/a
33	CEBPB	chr7:55862315-55862530	ECC-1	luminal epithelium:	n/a	chr7:55862399-55862410
34	RFX5	chr7:55862291-55862533	Hela-S3	cervix:	n/a	n/a
35	FOS	chr7:55862282-55862554	Hela-S3	cervix:	n/a	n/a
36	CEBPB	chr7:55862241-55862744	HCT-116	colon:	n/a	chr7:55862399-55862410
37	E2F4	chr7:55862320-55862554	MCF10A-Er-Src	breast:	n/a	n/a
38	CEBPB	chr7:55862358-55862505	IMR90	lung:	n/a	chr7:55862399-55862410
39	JUND	chr7:55862184-55862546	Hela-S3	cervix:	n/a	chr7:55862363-55862374
40	FOS	chr7:55862194-55862557	MCF10A-Er-Src	breast:	n/a	n/a
41	CEBPB	chr7:55862291-55862665	MCF-7	breast:	n/a	chr7:55862399-55862410
42	CEBPB	chr7:55862272-55862668	MCF-7	breast:	n/a	chr7:55862399-55862410
43	FOSL2	chr7:55862155-55862523	HepG2	liver:	n/a	chr7:55862362-55862373
44	TCF7L2	chr7:55862317-55862517	Hela-S3	cervix:	n/a	n/a
45	MAFF	chr7:55862329-55862495	HepG2	liver:	n/a	n/a
46	JUND	chr7:55862304-55862426	HepG2	liver:	n/a	chr7:55862363-55862374
47	STAT3	chr7:55862270-55862554	MCF10A-Er-Src	breast:	n/a	n/a
48	JUND	chr7:55862334-55862446	K562	blood:	n/a	chr7:55862363-55862374
49	SMC3	chr7:55862319-55862521	Hela-S3	cervix:	n/a	n/a
50	CEBPB	chr7:55862253-55862555	K562	blood:	n/a	chr7:55862399-55862410

Variant related genes	Relation type
CICP12	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10229689	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10231455	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10233558	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10239220	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10242739	0.82[AMR][1000 genomes]
rs10243293	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10247994	0.81[AMR][1000 genomes]
rs10257760	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10267471	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10268024	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11761500	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11761678	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11765567	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11766051	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11971165	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11971848	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11976304	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11982736	0.84[ASN][1000 genomes]
rs1910843	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28363703	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28641137	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28654591	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28670923	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4273806	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4388410	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4434572	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4523203	0.92[AMR][1000 genomes]
rs4577914	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4994531	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57339422	0.87[AMR][1000 genomes]
rs58154690	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58625047	0.85[AMR][1000 genomes]
rs6700	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6944683	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6945861	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6956609	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6959222	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6979201	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73350494	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73350500	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73352571	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7809922	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7810994	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv427782	chr7:55703073-56010314	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv888063	chr7:55728476-55899496	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
9	nsv469612	chr7:55752394-55876163	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv482609	chr7:55752394-55876163	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
12	nsv970835	chr7:55816398-55872502	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
14	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
15	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
16	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
17	nsv966928	chr7:55855289-55872502	Weak transcription ZNF genes & repeats	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6959347	PSPHP1	cis	Artery Tibial	GTEx
rs6959347	PSPHP1	cis	Heart Left Ventricle	GTEx
rs6959347	PSPHP1	cis	Nerve Tibial	GTEx
rs6959347	PSPHP1	cis	lung	GTEx
rs6959347	PSPHP1	cis	Adipose Subcutaneous	GTEx
rs6959347	PSPHP1	cis	Esophagus Muscularis	GTEx
rs6959347	PSPHP1	cis	Thyroid	GTEx
rs6959347	PSPHP1	cis	Muscle Skeletal	GTEx
rs6959347	PSPHP1	cis	Whole Blood	GTEx
rs6959347	PSPH	Cis_1M	lymphoblastoid	RTeQTL
rs6959347	PSPHP1	cis	Stomach	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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