Variant report

Variant	rs9261465
Chromosome Location	chr6:30103745-30103746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr6:30103438-30103914	HepG2	liver:	n/a	n/a
2	HNF4A	chr6:30103617-30103915	HepG2	liver:	n/a	chr6:30103749-30103764
3	FOXA1	chr6:30103468-30103944	HepG2	liver:	n/a	n/a
4	FOS	chr6:30103637-30104003	MCF10A-Er-Src	breast:	n/a	chr6:30103820-30103827
5	FOXA1	chr6:30103483-30103981	HepG2	liver:	n/a	n/a
6	STAT3	chr6:30103006-30104072	MCF10A-Er-Src	breast:	n/a	chr6:30103808-30103819
7	MYC	chr6:30103739-30103849	MCF10A-Er-Src	breast:	n/a	chr6:30103836-30103846
8	STAT3	chr6:30103533-30104070	MCF10A-Er-Src	breast:	n/a	chr6:30103808-30103819
9	CREB1	chr6:30103466-30104009	HepG2	liver:	n/a	n/a
10	FOXA2	chr6:30103511-30103867	A549	lung:	n/a	n/a
11	FOS	chr6:30103659-30103979	MCF10A-Er-Src	breast:	n/a	chr6:30103820-30103827
12	FOS	chr6:30103651-30103983	MCF10A-Er-Src	breast:	n/a	chr6:30103820-30103827
13	FOXA2	chr6:30103542-30103952	A549	lung:	n/a	n/a
14	EP300	chr6:30103487-30104050	HepG2	liver:	n/a	chr6:30103678-30103692
15	HNF4G	chr6:30103562-30103901	HepG2	liver:	n/a	n/a
16	STAT3	chr6:30103048-30104061	MCF10A-Er-Src	breast:	n/a	chr6:30103808-30103819
17	STAT1	chr6:30103601-30104031	Hela-S3	cervix:	n/a	chr6:30103808-30103819
18	FOXA1	chr6:30103482-30103958	HepG2	liver:	n/a	n/a
19	FOXA2	chr6:30103554-30103888	HepG2	liver:	n/a	n/a
20	EP300	chr6:30103466-30103884	HepG2	liver:	n/a	chr6:30103678-30103692
21	STAT3	chr6:30103689-30103816	MCF10A-Er-Src	breast:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30103696-30103746	NB4	blood:	n/a
2	chr6:30103696-30103746	K562	blood:	n/a
3	chr6:30103696-30103746	SKMC	muscle:	n/a
4	chr6:30103696-30103746	ProgFib	skin:	n/a
5	chr6:30103699-30103749	IMR90	lung:	fetal
6	chr6:30103696-30103746	CMK	blood:	n/a
7	chr6:30103699-30103749	ovcar-3	ovarian:	n/a
8	chr6:30103696-30103746	GM12892	blood:	n/a
9	chr6:30103699-30103749	SK-N-SH	brain:	n/a
10	chr6:30103699-30103749	HCT-116	colon:	n/a
11	chr6:30103696-30103746	SK-N-SH	brain:	n/a
12	chr6:30103699-30103749	GM06990	blood:	n/a
13	chr6:30103699-30103749	HCPEpiC	choroid plexus:	n/a
14	chr6:30103696-30103746	SK-N-SH_RA	brain:	n/a
15	chr6:30103696-30103746	U87	brain:	n/a
16	chr6:30103696-30103746	SK-N-MC	brain:	n/a
17	chr6:30103696-30103746	HRCEpiC	kidney:	n/a
18	chr6:30103699-30103749	HMEC	breast:	n/a
19	chr6:30103696-30103746	BJ	skin:	n/a
20	chr6:30103699-30103749	HPAEpiC	pulmonary alveolar:	n/a
21	chr6:30103696-30103746	GM06990	blood:	n/a
22	chr6:30103696-30103746	HRE	kidney:	n/a
23	chr6:30103699-30103749	T-47D	breast:	n/a
24	chr6:30103696-30103746	GM19239	blood:	n/a
25	chr6:30103699-30103749	PFSK-1	brain:	n/a
26	chr6:30103696-30103746	HIPEpiC	eye:	n/a
27	chr6:30103699-30103749	HRCEpiC	kidney:	n/a
28	chr6:30103699-30103749	AG04449	skin:	fetal
29	chr6:30103699-30103749	HepG2	liver:	n/a
30	chr6:30103699-30103749	CMK	blood:	n/a
31	chr6:30103699-30103749	AG09309	skin:	n/a
32	chr6:30103696-30103746	HL-60	blood:	n/a
33	chr6:30103699-30103749	U87	brain:	n/a
34	chr6:30103696-30103746	NHBE	bronchial:	n/a
35	chr6:30103699-30103749	K562	blood:	n/a
36	chr6:30103699-30103749	HL-60	blood:	n/a
37	chr6:30103696-30103746	MCF10A-Er-Src	breast:	n/a
38	chr6:30103699-30103749	NH-A	brain:	n/a
39	chr6:30103699-30103749	PANC-1	pancreas:	n/a
40	chr6:30103696-30103746	GM12878	blood:	n/a
41	chr6:30103696-30103746	NT2-D1	testis:	n/a
42	chr6:30103696-30103746	Caco-2	colon:	n/a
43	chr6:30103696-30103746	RPTEC	kidney:	n/a
44	chr6:30103696-30103746	GM12891	blood:	n/a
45	chr6:30103699-30103749	AG10803	skin:	n/a
46	chr6:30103696-30103746	AoSMC	blood vessel:	n/a
47	chr6:30103696-30103746	Hepatocyte	liver:	n/a
48	chr6:30103699-30103749	HRPEpiC	eye:	n/a
49	chr6:30103696-30103746	PANC-1	pancreas:	n/a
50	chr6:30103696-30103746	SAEC	small airway:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30028084..30030840-chr6:30103303..30105686,3	MCF-7	breast:
2	chr6:30097580..30101195-chr6:30103058..30105479,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252228	TF binding region
TRIM40	TF binding region
TRIM40	CpG island
ENSG00000252228	CpG island
ENSG00000204623	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000252228	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1042338	0.83[EUR][1000 genomes]
rs1076229	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947053	0.92[ASN][1000 genomes]
rs13194768	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1419671	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1419672	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1419673	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1541324	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1573297	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573298	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1573299	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17194607	0.80[EUR][1000 genomes]
rs2239530	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2284163	0.92[ASN][1000 genomes]
rs2285795	0.85[EUR][1000 genomes]
rs2285796	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2508030	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2508031	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517653	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517655	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28400887	0.86[ASN][1000 genomes]
rs2857433	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857435	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857436	0.90[ASN][1000 genomes]
rs2857438	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857440	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857458	0.90[ASN][1000 genomes]
rs3132124	0.81[ASN][1000 genomes]
rs3778622	0.81[EUR][1000 genomes]
rs3815079	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815080	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3815082	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3815084	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3815085	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3815086	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3888580	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4392759	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711211	0.81[EUR][1000 genomes]
rs4713293	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4959011	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4959012	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959041	0.92[ASN][1000 genomes]
rs4959044	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757259	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757261	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757262	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757263	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs757264	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7843	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261424	0.92[ASN][1000 genomes]
rs9261431	0.92[ASN][1000 genomes]
rs9261433	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261438	0.92[ASN][1000 genomes]
rs9261439	0.92[ASN][1000 genomes]
rs9261440	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261442	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261443	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261444	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261445	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261446	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261448	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261449	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261450	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261451	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9261453	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261454	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261455	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261456	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261457	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261458	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261459	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261461	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261462	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261466	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261470	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261472	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261479	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261480	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261481	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261482	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261483	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261484	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261485	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261486	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261488	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261489	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261490	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261491	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261492	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261493	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261495	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261496	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261497	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261498	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261499	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261500	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261501	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261502	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261503	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261504	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261505	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261507	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261508	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261509	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261511	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261512	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261513	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9261514	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9261516	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261517	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261518	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261519	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261521	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261522	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261523	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261524	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261525	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9261526	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261527	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261528	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261529	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261530	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261531	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261532	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261533	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261535	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs929156	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs957765	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9261465	HLA-A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30101400-30104000	Enhancers	Fetal Intestine Small	intestine
2	chr6:30101800-30105000	Enhancers	Fetal Intestine Large	intestine
3	chr6:30103200-30103800	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr6:30103200-30103800	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr6:30103200-30103800	Enhancers	Stomach Mucosa	stomach
6	chr6:30103400-30103800	Bivalent Enhancer	Placenta	Placenta
7	chr6:30103400-30103800	Bivalent Enhancer	Small Intestine	intestine
8	chr6:30103400-30103800	Flanking Active TSS	HepG2	liver
9	chr6:30103400-30104400	Enhancers	Hela-S3	cervix
10	chr6:30103400-30104600	Enhancers	Colonic Mucosa	Colon
11	chr6:30103600-30103800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
12	chr6:30103600-30104000	Enhancers	A549	lung
13	chr6:30103600-30104800	Enhancers	GM12878-XiMat	blood

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