Variant report

Variant	rs4729655
Chromosome Location	chr7:100701451-100701452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr7:100701158-100702071	SK-N-SH	brain:	n/a	n/a
2	REST	chr7:100701137-100702375	K562	blood:	n/a	n/a
3	REST	chr7:100701240-100702356	ECC-1	luminal epithelium:	n/a	n/a
4	REST	chr7:100701108-100702887	PANC-1	pancreas:	n/a	n/a
5	REST	chr7:100701372-100702052	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chr7:100701260-100702250	PANC-1	pancreas:	n/a	n/a
7	REST	chr7:100701285-100702411	ECC-1	luminal epithelium:	n/a	n/a
8	REST	chr7:100701205-100702164	U87	brain:	n/a	n/a
9	REST	chr7:100701186-100702385	HCT-116	colon:	n/a	n/a
10	JUND	chr7:100701185-100701462	HepG2	liver:	n/a	n/a
11	REST	chr7:100701093-100703065	HL-60	blood:	n/a	n/a
12	REST	chr7:100701401-100702030	Hela-S3	cervix:	n/a	n/a
13	REST	chr7:100701392-100702021	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr7:100701121-100702957	PFSK-1	brain:	n/a	n/a
15	REST	chr7:100701419-100702323	HepG2	liver:	n/a	n/a
16	REST	chr7:100701344-100702137	Hela-S3	cervix:	n/a	n/a
17	REST	chr7:100701401-100702160	HepG2	liver:	n/a	n/a
18	REST	chr7:100701430-100702336	H1-neurons	neurons:	n/a	n/a
19	REST	chr7:100701157-100702480	MCF-7	breast:	n/a	n/a
20	REST	chr7:100701272-100703070	A549	lung:	n/a	n/a
21	REST	chr7:100701249-100702245	PFSK-1	brain:	n/a	n/a
22	REST	chr7:100701187-100702455	PFSK-1	brain:	n/a	n/a
23	REST	chr7:100701393-100702414	HL-60	blood:	n/a	n/a
24	REST	chr7:100701418-100702325	PANC-1	pancreas:	n/a	n/a
25	REST	chr7:100701413-100702163	A549	lung:	n/a	n/a
26	TEAD4	chr7:100701448-100702094	A549	lung:	n/a	n/a
27	REST	chr7:100701317-100702106	MCF-7	breast:	n/a	n/a
28	REST	chr7:100701324-100702176	GM12878	blood:	n/a	n/a
29	REST	chr7:100701434-100702073	PANC-1	pancreas:	n/a	n/a
30	REST	chr7:100701338-100702462	HCT-116	colon:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100607173..100609796-chr7:100700740..100702978,2	K562	blood:
2	chr7:100493490..100497118-chr7:100701265..100703603,3	K562	blood:
3	chr7:100479669..100481601-chr7:100698885..100701717,2	K562	blood:
4	chr7:100422507..100425208-chr7:100700393..100702455,2	MCF-7	breast:
5	chr7:100492733..100496183-chr7:100699112..100703676,5	MCF-7	breast:
6	chr7:100694133..100697059-chr7:100699344..100702071,2	K562	blood:

No data

Variant related genes	Relation type
RN7SKP54	TF binding region
ENSG00000087085	Chromatin interaction
ENSG00000146828	Chromatin interaction
ENSG00000169894	Chromatin interaction
ENSG00000169876	Chromatin interaction
ENSG00000087087	Chromatin interaction
ENSG00000225946	Chromatin interaction
ENSG00000196411	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11976643	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11977541	0.82[EUR][1000 genomes]
rs11977544	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11981140	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13235027	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34957187	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4236553	0.86[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs4268055	0.83[ASN][1000 genomes]
rs4395825	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4515479	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4729656	0.86[CHB][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs55710224	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55903219	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56721881	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57645356	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58360470	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6465781	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6465784	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7777383	0.91[EUR][1000 genomes]
rs7780496	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7797230	0.87[ASW][hapmap];1.00[CEU][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv1826021	chr7:100525848-100749246	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1846644	chr7:100525848-100749246	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1822460	chr7:100606044-100749246	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv427796	chr7:100606044-100749246	Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv428181	chr7:100606044-100749246	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv831074	chr7:100606051-100745532	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1031942	chr7:100606734-100788660	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	esv1833777	chr7:100632790-100800131	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv1033081	chr7:100669629-100771824	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	esv1811048	chr7:100675933-100730280	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
14	esv1831657	chr7:100675933-100730280	Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
15	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4729655	BRI3	cis	cerebellum	SCAN
rs4729655	OR2AE1	cis	cerebellum	SCAN
rs4729655	ZNF3	cis	cerebellum	SCAN
rs4729655	C7orf51	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100672200-100702400	Strong transcription	Duodenum Mucosa	Duodenum
2	chr7:100698600-100703000	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr7:100699000-100702600	Strong transcription	Fetal Intestine Large	intestine
4	chr7:100700600-100703200	Strong transcription	Fetal Intestine Small	intestine

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