Variant report

Variant	rs6967414
Chromosome Location	chr7:6749758-6749759
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr7:6749498-6749766	K562	blood:	n/a	n/a
2	RCOR1	chr7:6749500-6749773	HepG2	liver:	n/a	n/a
3	GABPA	chr7:6749475-6749886	MCF-7	breast:	n/a	n/a
4	GABPA	chr7:6749459-6749766	A549	lung:	n/a	n/a
5	ARID3A	chr7:6749446-6749789	HepG2	liver:	n/a	n/a
6	GABPA	chr7:6749546-6749767	HepG2	liver:	n/a	n/a
7	NFYA	chr7:6749474-6749776	Hela-S3	cervix:	n/a	n/a
8	YY1	chr7:6749598-6749778	HCT-116	colon:	n/a	n/a
9	NFIC	chr7:6749505-6749776	HepG2	liver:	n/a	n/a
10	MAX	chr7:6749453-6749890	HepG2	liver:	n/a	n/a
11	CBX3	chr7:6749453-6749879	K562	blood:	n/a	n/a
12	TBP	chr7:6749474-6749815	HepG2	liver:	n/a	n/a
13	GABPA	chr7:6749514-6749827	Hela-S3	cervix:	n/a	n/a
14	TBL1XR1	chr7:6749627-6749764	K562	blood:	n/a	n/a
15	FOXA1	chr7:6749299-6749811	HepG2	liver:	n/a	n/a
16	GABPA	chr7:6749434-6749836	K562	blood:	n/a	n/a
17	CBX3	chr7:6749454-6749792	K562	blood:	n/a	n/a
18	RUNX3	chr7:6749495-6749791	GM12878	blood:	n/a	n/a
19	SP1	chr7:6749277-6749968	HCT-116	colon:	n/a	n/a
20	TBL1XR1	chr7:6749509-6749826	K562	blood:	n/a	n/a
21	CHD2	chr7:6749610-6749810	HepG2	liver:	n/a	n/a
22	SETDB1	chr7:6749298-6749789	U2OS	brain:	n/a	n/a
23	CBX3	chr7:6749398-6749899	HCT-116	colon:	n/a	n/a
24	SP1	chr7:6749442-6749800	HepG2	liver:	n/a	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSPH10B2-1	chr7:6749757-6749869	NONHSAT119063

No data

Variant related genes	Relation type
PMS2CL	TF binding region
ZNF12	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11770065	0.82[ASN][1000 genomes]
rs11974158	0.87[ASN][1000 genomes]
rs11979878	0.93[ASN][1000 genomes]
rs11980762	0.87[ASN][1000 genomes]
rs12531541	0.92[ASN][1000 genomes]
rs12535850	0.81[ASN][1000 genomes]
rs2881352	0.95[ASN][1000 genomes]
rs3757481	0.93[ASN][1000 genomes]
rs3757482	1.00[ASN][1000 genomes]
rs3757483	1.00[ASN][1000 genomes]
rs60514449	0.95[ASN][1000 genomes]
rs62439702	0.95[ASN][1000 genomes]
rs62439703	0.88[ASN][1000 genomes]
rs62439704	0.88[ASN][1000 genomes]
rs62439719	0.88[ASN][1000 genomes]
rs62439720	0.87[ASN][1000 genomes]
rs6463576	0.97[ASN][1000 genomes]
rs6463578	0.90[ASN][1000 genomes]
rs6943677	0.87[ASN][1000 genomes]
rs6944332	0.87[ASN][1000 genomes]
rs6948965	0.85[ASN][1000 genomes]
rs6952131	0.82[ASN][1000 genomes]
rs6953825	0.84[ASN][1000 genomes]
rs6954012	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6958648	0.87[ASN][1000 genomes]
rs6968879	0.87[ASN][1000 genomes]
rs6969066	1.00[ASN][1000 genomes]
rs6971324	0.87[ASN][1000 genomes]
rs6971979	0.87[ASN][1000 genomes]
rs6972017	0.93[ASN][1000 genomes]
rs6974325	0.80[ASN][1000 genomes]
rs6975002	0.88[ASN][1000 genomes]
rs6979127	0.88[ASN][1000 genomes]
rs6979158	0.86[ASN][1000 genomes]
rs7782227	1.00[ASN][1000 genomes]
rs7786706	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7798471	0.92[ASN][1000 genomes]
rs7799134	0.87[ASN][1000 genomes]
rs7804259	0.82[ASN][1000 genomes]
rs9639027	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv887439	chr7:6736332-6791749	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1015646	chr7:6738483-6779270	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv887440	chr7:6743097-6820508	Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv887441	chr7:6744957-6919214	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	esv1819001	chr7:6746810-6785602	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv8039	chr7:6748111-6764886	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv10861	chr7:6749172-6768435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6967414	PMS2CL	cis	Esophagus Muscularis	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6747000-6768600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:6747400-6750600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:6747400-6752600	Weak transcription	HSMMtube	muscle
4	chr7:6747400-6757400	Weak transcription	Fetal Brain Female	brain
5	chr7:6748000-6749800	Active TSS	Liver	Liver
6	chr7:6749000-6749800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:6749600-6749800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr7:6749600-6750000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell

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