Variant report

Variant	rs9261468
Chromosome Location	chr6:30104480-30104481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr6:30104371-30104733	GM12878	blood:	n/a	n/a
2	RUNX3	chr6:30104208-30104850	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:30104337-30104806	GM12878	blood:	n/a	n/a
4	NFIC	chr6:30104259-30104759	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30104440-30104490	PANC-1	pancreas:	n/a
2	chr6:30104440-30104490	AG04450	lung:	fetal
3	chr6:30104440-30104490	AG09319	gingival:	n/a
4	chr6:30104440-30104490	NB4	blood:	n/a
5	chr6:30104440-30104490	HEEpiC	esophagus:	n/a
6	chr6:30104440-30104490	HUVEC	blood vessel:	n/a
7	chr6:30104440-30104490	NT2-D1	testis:	n/a
8	chr6:30104440-30104490	RPTEC	kidney:	n/a
9	chr6:30104440-30104490	HCPEpiC	choroid plexus:	n/a
10	chr6:30104440-30104490	U87	brain:	n/a
11	chr6:30104440-30104490	PrEC	prostate:	n/a
12	chr6:30104440-30104490	HCT-116	colon:	n/a
13	chr6:30104440-30104490	HNPCEpiC	eye:	n/a
14	chr6:30104440-30104490	CMK	blood:	n/a
15	chr6:30104440-30104490	GM12878	blood:	n/a
16	chr6:30104440-30104490	IMR90	lung:	fetal
17	chr6:30104440-30104490	HMEC	breast:	n/a
18	chr6:30104440-30104490	SKMC	muscle:	n/a
19	chr6:30104440-30104490	GM12891	blood:	n/a
20	chr6:30104440-30104490	HIPEpiC	eye:	n/a
21	chr6:30104440-30104490	H1-hESC	embryonic stem cell:	embryo
22	chr6:30104440-30104490	Caco-2	colon:	n/a
23	chr6:30104440-30104490	LNCaP	prostate:	n/a
24	chr6:30104440-30104490	MCF10A-Er-Src	breast:	n/a
25	chr6:30104440-30104490	HPAEpiC	pulmonary alveolar:	n/a
26	chr6:30104440-30104490	AG10803	skin:	n/a
27	chr6:30104440-30104490	GM06990	blood:	n/a
28	chr6:30104440-30104490	AG09309	skin:	n/a
29	chr6:30104440-30104490	HCM	heart:	n/a
30	chr6:30104440-30104490	NHBE	bronchial:	n/a
31	chr6:30104440-30104490	Jurkat	blood:	n/a
32	chr6:30104440-30104490	BE2_C	brain:	n/a
33	chr6:30104440-30104490	HL-60	blood:	n/a
34	chr6:30104440-30104490	SAEC	small airway:	n/a
35	chr6:30104440-30104490	AoSMC	blood vessel:	n/a
36	chr6:30104440-30104490	GM19239	blood:	n/a
37	chr6:30104440-30104490	HRCEpiC	kidney:	n/a
38	chr6:30104440-30104490	MCF-7	breast:	n/a
39	chr6:30104440-30104490	HEK293	kidney:	embryo
40	chr6:30104440-30104490	NH-A	brain:	n/a
41	chr6:30104440-30104490	AG04449	skin:	fetal
42	chr6:30104440-30104490	HRPEpiC	eye:	n/a
43	chr6:30104440-30104490	ECC-1	luminal epithelium:	n/a
44	chr6:30104440-30104490	ovcar-3	ovarian:	n/a
45	chr6:30104440-30104490	SK-N-MC	brain:	n/a
46	chr6:30104440-30104490	Hela-S3	cervix:	n/a
47	chr6:30104440-30104490	SK-N-SH_RA	brain:	n/a
48	chr6:30104440-30104490	T-47D	breast:	n/a
49	chr6:30104440-30104490	NHDF-neo	bronchial:	n/a
50	chr6:30104440-30104490	ProgFib	skin:	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
TRIM40	TF binding region
ENSG00000252228	TF binding region
ENSG00000252228	CpG island
TRIM40	CpG island
ENSG00000066379	Chromatin interaction
ENSG00000252228	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 5 )

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]
rs9261465	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]
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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9261468	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs9261468	ZKSCAN3	cis	cerebellum	SCAN
rs9261468	BTN2A1	cis	cerebellum	SCAN
rs9261468	HIST1H2BN	cis	parietal	SCAN
rs9261468	HIST1H2AM	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30101800-30105000	Enhancers	Fetal Intestine Large	intestine
2	chr6:30103400-30104600	Enhancers	Colonic Mucosa	Colon
3	chr6:30103600-30104800	Enhancers	GM12878-XiMat	blood
4	chr6:30103800-30105000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:30103800-30105000	Enhancers	Small Intestine	intestine
6	chr6:30103800-30105400	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr6:30103800-30105400	Enhancers	HepG2	liver
8	chr6:30103800-30107400	Active TSS	Placenta	Placenta
9	chr6:30104000-30104600	Active TSS	Duodenum Mucosa	Duodenum
10	chr6:30104000-30104800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:30104000-30104800	Flanking Active TSS	Fetal Intestine Small	intestine
12	chr6:30104200-30104600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:30104200-30104600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr6:30104200-30104800	Enhancers	Primary hematopoietic stem cells	blood
15	chr6:30104200-30106400	Weak transcription	Stomach Mucosa	stomach
16	chr6:30104400-30104800	Enhancers	Rectal Mucosa Donor 29	rectum

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