Variant report

Variant	rs2857458
Chromosome Location	chr6:30104783-30104784
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:1)
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	POLR2A	chr6:30104770-30105003	MCF-7	breast:	n/a	n/a
2	RUNX3	chr6:30104208-30104850	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:30104642-30104821	MCF10A-Er-Src	breast:	n/a	n/a
4	RUNX3	chr6:30104337-30104806	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30104754-30104804	ECC-1	luminal epithelium:	n/a
2	chr6:30104754-30104804	Jurkat	blood:	n/a
3	chr6:30104754-30104804	HepG2	liver:	n/a
4	chr6:30104754-30104804	AG04450	lung:	fetal
5	chr6:30104754-30104804	HCPEpiC	choroid plexus:	n/a
6	chr6:30104754-30104804	ProgFib	skin:	n/a
7	chr6:30104754-30104804	Caco-2	colon:	n/a
8	chr6:30104754-30104804	ovcar-3	ovarian:	n/a
9	chr6:30104754-30104804	AG10803	skin:	n/a
10	chr6:30104754-30104804	HCF	heart:	n/a
11	chr6:30104754-30104804	A549	lung:	n/a
12	chr6:30104754-30104804	HL-60	blood:	n/a
13	chr6:30104754-30104804	HCT-116	colon:	n/a
14	chr6:30104754-30104804	NHDF-neo	bronchial:	n/a
15	chr6:30104754-30104804	GM12878	blood:	n/a
16	chr6:30104754-30104804	IMR90	lung:	fetal
17	chr6:30104754-30104804	HAEpiC	amniotic membrane:	n/a
18	chr6:30104754-30104804	CMK	blood:	n/a
19	chr6:30104754-30104804	GM06990	blood:	n/a
20	chr6:30104754-30104804	PrEC	prostate:	n/a
21	chr6:30104754-30104804	Hepatocyte	liver:	n/a
22	chr6:30104754-30104804	MCF-7	breast:	n/a
23	chr6:30104754-30104804	BE2_C	brain:	n/a
24	chr6:30104754-30104804	NHBE	bronchial:	n/a
25	chr6:30104754-30104804	HRE	kidney:	n/a
26	chr6:30104754-30104804	U87	brain:	n/a
27	chr6:30104754-30104804	SKMC	muscle:	n/a
28	chr6:30104754-30104804	HMEC	breast:	n/a
29	chr6:30104754-30104804	NT2-D1	testis:	n/a
30	chr6:30104754-30104804	BJ	skin:	n/a
31	chr6:30104754-30104804	LNCaP	prostate:	n/a
32	chr6:30104754-30104804	GM12892	blood:	n/a
33	chr6:30104754-30104804	HRPEpiC	eye:	n/a
34	chr6:30104754-30104804	PFSK-1	brain:	n/a
35	chr6:30104754-30104804	HRCEpiC	kidney:	n/a
36	chr6:30104754-30104804	SK-N-SH_RA	brain:	n/a
37	chr6:30104754-30104804	AG09309	skin:	n/a
38	chr6:30104754-30104804	HNPCEpiC	eye:	n/a
39	chr6:30104754-30104804	PANC-1	pancreas:	n/a
40	chr6:30104754-30104804	AG04449	skin:	fetal
41	chr6:30104754-30104804	HPAEpiC	pulmonary alveolar:	n/a
42	chr6:30104754-30104804	SK-N-MC	brain:	n/a
43	chr6:30104754-30104804	Hela-S3	cervix:	n/a
44	chr6:30104754-30104804	HCM	heart:	n/a
45	chr6:30104754-30104804	HEK293	kidney:	embryo
46	chr6:30104754-30104804	GM19239	blood:	n/a
47	chr6:30104754-30104804	H1-hESC	embryonic stem cell:	embryo
48	chr6:30104754-30104804	NH-A	brain:	n/a
49	chr6:30104754-30104804	HEEpiC	esophagus:	n/a
50	chr6:30104754-30104804	HIPEpiC	eye:	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:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM15-1	chr6:30104510-30104975	NONHSAT108605

No data

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

Extended variants
information (count: 124 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1076229	0.85[ASN][1000 genomes]
rs10947053	0.82[ASN][1000 genomes]
rs1419671	0.85[ASN][1000 genomes]
rs1419672	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1419673	0.83[ASN][1000 genomes]
rs1541324	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1573297	0.90[ASN][1000 genomes]
rs1573298	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573299	0.90[ASN][1000 genomes]
rs2284163	0.82[ASN][1000 genomes]
rs2285796	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2508030	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2508031	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517653	0.88[ASN][1000 genomes]
rs2517655	0.87[ASN][1000 genomes]
rs28400887	0.82[ASN][1000 genomes]
rs2857433	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2857435	0.94[ASN][1000 genomes]
rs2857436	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857438	0.94[ASN][1000 genomes]
rs2857439	0.90[ASN][1000 genomes]
rs2857440	0.94[ASN][1000 genomes]
rs3132124	0.82[ASN][1000 genomes]
rs3815079	0.88[ASN][1000 genomes]
rs3815080	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815082	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3815084	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3815085	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3815086	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3888580	0.85[ASN][1000 genomes]
rs4392759	0.90[ASN][1000 genomes]
rs4713293	0.83[ASN][1000 genomes]
rs4959011	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959012	0.90[ASN][1000 genomes]
rs4959041	0.82[ASN][1000 genomes]
rs4959044	0.90[ASN][1000 genomes]
rs757259	0.90[ASN][1000 genomes]
rs757261	0.90[ASN][1000 genomes]
rs757262	0.90[ASN][1000 genomes]
rs757263	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs757264	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261424	0.82[ASN][1000 genomes]
rs9261431	0.82[ASN][1000 genomes]
rs9261433	0.83[ASN][1000 genomes]
rs9261438	0.82[ASN][1000 genomes]
rs9261439	0.82[ASN][1000 genomes]
rs9261440	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9261442	0.83[ASN][1000 genomes]
rs9261443	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261444	0.83[ASN][1000 genomes]
rs9261445	0.83[ASN][1000 genomes]
rs9261446	0.83[ASN][1000 genomes]
rs9261449	0.85[ASN][1000 genomes]
rs9261450	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261451	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9261453	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261454	0.86[ASN][1000 genomes]
rs9261455	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9261456	0.86[ASN][1000 genomes]
rs9261457	0.86[ASN][1000 genomes]
rs9261458	0.86[ASN][1000 genomes]
rs9261459	0.86[ASN][1000 genomes]
rs9261461	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261462	0.90[ASN][1000 genomes]
rs9261463	0.90[ASN][1000 genomes]
rs9261465	0.90[ASN][1000 genomes]
rs9261466	0.94[ASN][1000 genomes]
rs9261467	0.90[ASN][1000 genomes]
rs9261468	0.90[ASN][1000 genomes]
rs9261470	0.94[ASN][1000 genomes]
rs9261471	0.90[ASN][1000 genomes]
rs9261472	0.94[ASN][1000 genomes]
rs9261473	0.90[ASN][1000 genomes]
rs9261479	0.93[ASN][1000 genomes]
rs9261480	0.93[ASN][1000 genomes]
rs9261481	0.89[ASN][1000 genomes]
rs9261482	0.94[ASN][1000 genomes]
rs9261483	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261484	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9261485	0.94[ASN][1000 genomes]
rs9261486	0.94[ASN][1000 genomes]
rs9261488	0.90[ASN][1000 genomes]
rs9261489	0.90[ASN][1000 genomes]
rs9261490	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261491	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261492	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261493	0.93[ASN][1000 genomes]
rs9261495	0.90[ASN][1000 genomes]
rs9261496	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261497	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261498	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261499	0.90[ASN][1000 genomes]
rs9261500	0.90[ASN][1000 genomes]
rs9261501	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261502	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261503	0.90[ASN][1000 genomes]
rs9261504	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261505	0.90[ASN][1000 genomes]
rs9261507	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261508	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261509	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261511	0.90[ASN][1000 genomes]
rs9261512	0.89[ASN][1000 genomes]
rs9261513	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261514	0.89[ASN][1000 genomes]
rs9261516	0.87[ASN][1000 genomes]
rs9261517	0.90[ASN][1000 genomes]
rs9261518	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261519	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261521	0.87[ASN][1000 genomes]
rs9261522	0.87[ASN][1000 genomes]
rs9261523	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261524	0.90[ASN][1000 genomes]
rs9261525	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9261526	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261527	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261528	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261529	0.91[ASN][1000 genomes]
rs9261530	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261531	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261532	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9261533	0.91[ASN][1000 genomes]
rs9261535	0.83[ASN][1000 genomes]
rs929156	0.83[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2857458	HIST1H2BN	cis	parietal	SCAN
rs2857458	GRM4	cis	parietal	SCAN
rs2857458	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs2857458	HIST1H2AM	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30101800-30105000	Enhancers	Fetal Intestine Large	intestine
2	chr6:30103600-30104800	Enhancers	GM12878-XiMat	blood
3	chr6:30103800-30105000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:30103800-30105000	Enhancers	Small Intestine	intestine
5	chr6:30103800-30105400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:30103800-30105400	Enhancers	HepG2	liver
7	chr6:30103800-30107400	Active TSS	Placenta	Placenta
8	chr6:30104000-30104800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:30104000-30104800	Flanking Active TSS	Fetal Intestine Small	intestine
10	chr6:30104200-30104800	Enhancers	Primary hematopoietic stem cells	blood
11	chr6:30104200-30106400	Weak transcription	Stomach Mucosa	stomach
12	chr6:30104400-30104800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr6:30104600-30104800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:30104600-30105000	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr6:30104600-30105000	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
16	chr6:30104600-30105200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr6:30104600-30105400	Active TSS	Colonic Mucosa	Colon

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