Variant report

Variant	rs3027041
Chromosome Location	chr1:159181560-159181561
allele	C/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	CTCF	chr1:159181440-159181590	GM12878	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
2	RAD21	chr1:159181296-159181636	GM12878	blood:	n/a	chr1:159181502-159181521
3	CTCF	chr1:159181460-159181610	GM12871	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
4	CTCF	chr1:159181440-159181590	BJ	skin:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
5	RAD21	chr1:159181279-159181682	ECC-1	luminal epithelium:	n/a	chr1:159181502-159181521
6	RAD21	chr1:159181307-159181652	K562	blood:	n/a	chr1:159181502-159181521
7	CTCF	chr1:159181370-159181767	HUVEC	blood vessel:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
8	CTCF	chr1:159180633-159181935	A549	lung:	n/a	chr1:159181190-159181199 chr1:159181499-159181520 chr1:159181187-159181205 chr1:159181504-159181522
9	CTCF	chr1:159181440-159181590	GM12868	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
10	ZNF143	chr1:159181357-159181710	K562	blood:	n/a	n/a
11	MAFK	chr1:159181414-159181657	K562	blood:	n/a	chr1:159181522-159181538 chr1:159181520-159181540
12	CTCF	chr1:159181420-159181570	GM12868	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
13	CTCF	chr1:159181398-159181586	SK-N-SH_RA	brain:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
14	CTCF	chr1:159181375-159181649	NHEK	skin:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
15	CTCF	chr1:159181440-159181590	AG04449	skin:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
16	CTCF	chr1:159181420-159181570	GM12873	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
17	REST	chr1:159181371-159181565	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr1:159181378-159181650	GM10266	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
19	CTCF	chr1:159181335-159181698	K562	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
20	RAD21	chr1:159181342-159181688	A549	lung:	n/a	chr1:159181502-159181521
21	RAD21	chr1:159181149-159181714	GM12878	blood:	n/a	chr1:159181502-159181521
22	CTCF	chr1:159181394-159181633	MCF-7	breast:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
23	CTCF	chr1:159181440-159181590	HCPEpiC	choroid plexus:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
24	GTF2F1	chr1:159181399-159181599	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr1:159181420-159181570	HL-60	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
26	CTCF	chr1:159181440-159181590	HUVEC	blood vessel:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
27	ELF1	chr1:159181376-159181582	GM12878	blood:	n/a	n/a
28	RAD21	chr1:159181309-159181663	SK-N-SH_RA	brain:	n/a	chr1:159181502-159181521
29	CTCF	chr1:159181420-159181570	HA-sp	spinal cord:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
30	CTCF	chr1:159181440-159181590	GM12871	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
31	CTCF	chr1:159181386-159181618	MCF-7	breast:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
32	CTCF	chr1:159181372-159181617	Fibrobl	skin:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
33	CTCF	chr1:159181420-159181570	BE2_C	brain:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
34	CTCF	chr1:159181390-159181652	Hela-S3	cervix:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
35	CTCF	chr1:159181420-159181570	MCF-7	breast:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
36	CTCF	chr1:159181440-159181590	HVMF	connective:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
37	CTCF	chr1:159181405-159181698	GM13976	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
38	CTCF	chr1:159181420-159181570	GM12866	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
39	CTCF	chr1:159181278-159181642	H1-hESC	embryonic stem cell:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
40	CTCF	chr1:159181440-159181590	HRPEpiC	eye:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
41	CTCF	chr1:159181440-159181590	GM12801	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
42	SMC3	chr1:159181358-159181700	HepG2	liver:	n/a	chr1:159181506-159181520
43	CTCF	chr1:159181387-159181654	LNCaP	prostate:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
44	RCOR1	chr1:159181289-159181583	K562	blood:	n/a	n/a
45	CTCF	chr1:159181420-159181570	NHLF	lung:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
46	CTCF	chr1:159181420-159181570	GM12867	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
47	CTCF	chr1:159181393-159181642	Lung_OC	lung:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
48	RAD21	chr1:159181362-159181641	K562	blood:	n/a	chr1:159181502-159181521
49	CTCF	chr1:159181460-159181610	GM12865	blood:	n/a	chr1:159181499-159181520 chr1:159181504-159181522
50	CEBPB	chr1:159181152-159181598	H1-hESC	embryonic stem cell:	n/a	chr1:159181329-159181342 chr1:159181329-159181342 chr1:159181329-159181342 chr1:159181329-159181340

No.	Distal block	Cell Line	Cell type
1	chr1:159130520..159131495-chr1:159180884..159182144,24	K562	blood:
2	chr1:159129691..159131233-chr1:159180012..159181804,2	MCF-7	breast:
3	chr1:159174604..159177754-chr1:159180035..159182676,3	K562	blood:
4	chr1:159101820..159102345-chr1:159180944..159181952,4	MCF-7	breast:
5	chr1:159129289..159129912-chr1:159181140..159181994,2	MCF-7	breast:
6	chr1:159130498..159131890-chr1:159181009..159182449,9	MCF-7	breast:
7	chr1:159101858..159102727-chr1:159181553..159182280,2	MCF-7	breast:
8	chr1:159131846..159132446-chr1:159181062..159181654,2	MCF-7	breast:
9	chr1:159101871..159102754-chr1:159180441..159181987,6	K562	blood:
10	chr1:159167007..159168193-chr1:159181056..159182026,4	MCF-7	breast:
11	chr1:159090280..159090949-chr1:159180874..159181620,2	MCF-7	breast:
12	chr1:159130523..159131496-chr1:159179878..159182456,22	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225670	TF binding region
ENSG00000213088	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10047107	1.00[EUR][1000 genomes]
rs10437336	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10437337	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10489847	1.00[EUR][1000 genomes]
rs10489850	1.00[EUR][1000 genomes]
rs10489851	1.00[EUR][1000 genomes]
rs10489852	1.00[EUR][1000 genomes]
rs10489853	1.00[EUR][1000 genomes]
rs11265143	0.82[AFR][1000 genomes]
rs11265145	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11265147	1.00[EUR][1000 genomes]
rs11265148	1.00[EUR][1000 genomes]
rs11265151	1.00[EUR][1000 genomes]
rs11265153	1.00[EUR][1000 genomes]
rs11265167	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12057331	1.00[EUR][1000 genomes]
rs12060241	1.00[EUR][1000 genomes]
rs12062367	1.00[EUR][1000 genomes]
rs12063682	1.00[EUR][1000 genomes]
rs12063973	1.00[EUR][1000 genomes]
rs12064129	1.00[EUR][1000 genomes]
rs12064962	1.00[EUR][1000 genomes]
rs12067678	1.00[EUR][1000 genomes]
rs12068030	1.00[EUR][1000 genomes]
rs12068651	1.00[EUR][1000 genomes]
rs12074418	1.00[EUR][1000 genomes]
rs12074452	1.00[EUR][1000 genomes]
rs12074934	1.00[EUR][1000 genomes]
rs12078114	1.00[EUR][1000 genomes]
rs12078168	1.00[EUR][1000 genomes]
rs12079229	1.00[EUR][1000 genomes]
rs12079235	1.00[EUR][1000 genomes]
rs12082893	1.00[EUR][1000 genomes]
rs12085001	1.00[EUR][1000 genomes]
rs12085085	1.00[EUR][1000 genomes]
rs12085686	1.00[EUR][1000 genomes]
rs12086637	1.00[EUR][1000 genomes]
rs12086871	1.00[EUR][1000 genomes]
rs12087366	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095599	1.00[EUR][1000 genomes]
rs12096257	1.00[EUR][1000 genomes]
rs13374880	1.00[EUR][1000 genomes]
rs16841729	1.00[EUR][1000 genomes]
rs16841784	1.00[EUR][1000 genomes]
rs16841789	1.00[EUR][1000 genomes]
rs16841937	1.00[EUR][1000 genomes]
rs16841970	1.00[EUR][1000 genomes]
rs16842041	1.00[EUR][1000 genomes]
rs2325923	1.00[EUR][1000 genomes]
rs2325925	1.00[EUR][1000 genomes]
rs2325927	1.00[EUR][1000 genomes]
rs2746042	1.00[EUR][1000 genomes]
rs2746043	1.00[TSI][hapmap]
rs2746044	1.00[TSI][hapmap]
rs2814755	1.00[TSI][hapmap]
rs2852717	1.00[TSI][hapmap]
rs2852719	1.00[TSI][hapmap]
rs28537540	1.00[EUR][1000 genomes]
rs3026944	1.00[EUR][1000 genomes]
rs3026947	1.00[EUR][1000 genomes]
rs3026970	1.00[EUR][1000 genomes]
rs3026984	1.00[EUR][1000 genomes]
rs3027031	0.82[AFR][1000 genomes]
rs3027040	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3027046	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3027047	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3027050	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3027054	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs3027057	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3027066	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34152791	1.00[EUR][1000 genomes]
rs34870435	1.00[EUR][1000 genomes]
rs35122728	1.00[EUR][1000 genomes]
rs36103299	1.00[EUR][1000 genomes]
rs36160848	1.00[EUR][1000 genomes]
rs3893415	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4255380	1.00[EUR][1000 genomes]
rs4534374	1.00[EUR][1000 genomes]
rs4568831	1.00[EUR][1000 genomes]
rs56113018	1.00[EUR][1000 genomes]
rs59437380	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6656586	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6670082	1.00[EUR][1000 genomes]
rs6670592	1.00[EUR][1000 genomes]
rs6670703	1.00[EUR][1000 genomes]
rs6673514	1.00[EUR][1000 genomes]
rs6695631	1.00[EUR][1000 genomes]
rs6696230	1.00[EUR][1000 genomes]
rs73023773	1.00[EUR][1000 genomes]
rs73023775	1.00[EUR][1000 genomes]
rs73027932	1.00[EUR][1000 genomes]
rs74122265	1.00[EUR][1000 genomes]
rs7515532	1.00[EUR][1000 genomes]
rs7552141	1.00[EUR][1000 genomes]
rs856059	1.00[EUR][1000 genomes]
rs856060	1.00[EUR][1000 genomes]
rs856061	1.00[EUR][1000 genomes]
rs856062	1.00[EUR][1000 genomes]
rs856063	1.00[EUR][1000 genomes]
rs856065	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs856069	1.00[EUR][1000 genomes]
rs856078	1.00[EUR][1000 genomes]
rs864439	1.00[EUR][1000 genomes]

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159158800-159188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:159178200-159182200	Weak transcription	Spleen	Spleen
3	chr1:159178200-159188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:159180600-159181800	Enhancers	A549	lung
5	chr1:159181000-159181600	Enhancers	HSMMtube	muscle
6	chr1:159181000-159181800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:159181000-159182000	Enhancers	HSMM	muscle
8	chr1:159181200-159181600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:159181200-159181600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:159181200-159181600	Flanking Active TSS	HUVEC	blood vessel
11	chr1:159181400-159181600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
12	chr1:159181400-159182400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:159181400-159188400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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