Variant report

Variant	rs9292877
Chromosome Location	chr5:43401980-43401981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:43401960-43402110	NB4	blood:	n/a	n/a
2	RAD21	chr5:43401942-43402294	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr5:43401485-43402480	A549	lung:	n/a	n/a
4	RCOR1	chr5:43401962-43402220	K562	blood:	n/a	n/a
5	CTCF	chr5:43401960-43402110	GM12868	blood:	n/a	n/a
6	CTCF	chr5:43401980-43402130	GM12874	blood:	n/a	n/a
7	MAZ	chr5:43401975-43402228	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr5:43401851-43402333	MCF-7	breast:	n/a	n/a
9	RAD21	chr5:43401875-43402317	HepG2	liver:	n/a	n/a
10	RAD21	chr5:43401963-43402259	H1-hESC	embryonic stem cell:	n/a	n/a
11	GATA3	chr5:43401897-43402266	T-47D	breast:	n/a	n/a
12	RAD21	chr5:43401908-43402315	HepG2	liver:	n/a	n/a
13	RAD21	chr5:43401968-43402192	SK-N-SH_RA	brain:	n/a	n/a
14	MAX	chr5:43401928-43402327	K562	blood:	n/a	n/a
15	SMC3	chr5:43401972-43402299	HepG2	liver:	n/a	n/a
16	GTF2F1	chr5:43401953-43402318	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr5:43401975-43402243	GM12878	blood:	n/a	n/a
18	CTCF	chr5:43401980-43402217	A549	lung:	n/a	n/a
19	CTCF	chr5:43401907-43402326	K562	blood:	n/a	n/a
20	CTCF	chr5:43401980-43402130	HCM	heart:	n/a	n/a
21	CTCF	chr5:43401952-43402341	HepG2	liver:	n/a	n/a
22	CTCF	chr5:43401914-43402291	K562	blood:	n/a	n/a
23	USF2	chr5:43401880-43402338	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr5:43401936-43402277	HepG2	liver:	n/a	n/a
25	RAD21	chr5:43401955-43402240	K562	blood:	n/a	n/a
26	CTCF	chr5:43401933-43402273	K562	blood:	n/a	n/a
27	CTCF	chr5:43401980-43402130	WI-38	lung:	n/a	n/a
28	RFX5	chr5:43401934-43402278	Hela-S3	cervix:	n/a	chr5:43402086-43402101
29	CTCF	chr5:43401980-43402130	K562	blood:	n/a	n/a
30	CTCF	chr5:43401860-43402010	HAc	cerebellar:	n/a	n/a
31	RAD21	chr5:43401821-43402281	A549	lung:	n/a	n/a
32	SMC3	chr5:43401915-43402331	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr5:43401971-43402200	SK-N-SH_RA	brain:	n/a	n/a
34	CTCF	chr5:43401909-43402218	K562	blood:	n/a	n/a
35	CTCF	chr5:43401971-43402249	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43064153..43067001-chr5:43400205..43402124,2	K562	blood:
2	chr5:43395776..43403836-chr5:43482661..43487155,15	MCF-7	breast:
3	chr5:43399926..43401984-chr5:43482652..43484625,3	K562	blood:
4	chr5:43400613..43403183-chr5:43554881..43557703,2	MCF-7	breast:
5	chr5:43398637..43404143-chr5:43481703..43486799,11	MCF-7	breast:
6	chr5:43401279..43403730-chr5:43426630..43430276,3	MCF-7	breast:
7	chr5:43401145..43403362-chr5:43418703..43420917,2	MCF-7	breast:

No data

Variant related genes	Relation type
CCL28	TF binding region
ENSG00000151881	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000249492	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10043868	1.00[ASN][1000 genomes]
rs10044795	0.94[ASN][1000 genomes]
rs10044799	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055041	0.81[ASN][1000 genomes]
rs10062256	1.00[ASN][1000 genomes]
rs1025299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461740	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10473309	0.97[ASN][1000 genomes]
rs1083833	0.94[ASN][1000 genomes]
rs10941642	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12656650	1.00[JPT][hapmap]
rs12657635	1.00[JPT][hapmap]
rs12657724	1.00[JPT][hapmap]
rs12659627	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs13155622	1.00[MEX][hapmap]
rs13155888	1.00[JPT][hapmap]
rs13160431	1.00[JPT][hapmap]
rs13164705	1.00[ASN][1000 genomes]
rs13165869	1.00[JPT][hapmap]
rs13168053	1.00[JPT][hapmap]
rs13169908	0.85[CHB][hapmap]
rs13173517	1.00[JPT][hapmap]
rs13186439	0.85[CHB][hapmap]
rs16873319	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2042950	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs28461402	1.00[ASN][1000 genomes]
rs34060183	1.00[ASN][1000 genomes]
rs34880892	0.97[ASN][1000 genomes]
rs35001439	0.97[ASN][1000 genomes]
rs35446538	0.97[ASN][1000 genomes]
rs36000604	0.91[ASN][1000 genomes]
rs36025143	1.00[ASN][1000 genomes]
rs36062172	0.91[ASN][1000 genomes]
rs36063200	1.00[ASN][1000 genomes]
rs3733767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756417	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3797152	1.00[ASN][1000 genomes]
rs3797153	1.00[ASN][1000 genomes]
rs3806871	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs3822423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264950	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs4438885	1.00[JPT][hapmap]
rs4498257	1.00[JPT][hapmap]
rs4533897	1.00[JPT][hapmap]
rs6451687	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451688	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861429	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865915	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6866007	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6868939	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6878207	0.91[ASN][1000 genomes]
rs6889653	1.00[JPT][hapmap]
rs6890108	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6892337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71590642	1.00[ASN][1000 genomes]
rs71610306	0.97[ASN][1000 genomes]
rs71629107	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720858	1.00[JPT][hapmap];1.00[MEX][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9292877	NNT	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43397000-43404000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:43397400-43402000	Weak transcription	Gastric	stomach
3	chr5:43397400-43402800	Weak transcription	Stomach Mucosa	stomach
4	chr5:43397400-43410200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:43397600-43402000	Weak transcription	Pancreas	Pancrea
6	chr5:43397600-43402000	Weak transcription	A549	lung
7	chr5:43397600-43409400	Weak transcription	Colonic Mucosa	Colon
8	chr5:43398000-43409000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:43398000-43409400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:43401200-43402200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr5:43401400-43402200	Enhancers	Hela-S3	cervix
12	chr5:43401600-43402000	Weak transcription	Esophagus	oesophagus
13	chr5:43401600-43402000	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links