Variant report

Variant	rs9261424
Chromosome Location	chr6:30080994-30080995
allele	C/G
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	GATA3	chr6:30080728-30081344	MCF-7	breast:	n/a	chr6:30080737-30080747
2	RELA	chr6:30080489-30081505	GM19193	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
3	HNF4A	chr6:30080797-30081134	HepG2	liver:	n/a	chr6:30080912-30080927 chr6:30080913-30080927 chr6:30080914-30080926 chr6:30080913-30080927 chr6:30081089-30081102 chr6:30080918-30080926 chr6:30080912-30080927 chr6:30080914-30080926 chr6:30081089-30081102 chr6:30080913-30080925 chr6:30080914-30080926 chr6:30080911-30080929 chr6:30080913-30080926 chr6:30080912-30080927 chr6:30080914-30080927
4	SP1	chr6:30080827-30081252	GM12878	blood:	n/a	n/a
5	RELA	chr6:30080835-30081422	GM19099	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
6	TCF12	chr6:30080679-30081230	A549	lung:	n/a	n/a
7	HNF4G	chr6:30080794-30081156	HepG2	liver:	n/a	chr6:30080912-30080927 chr6:30080913-30080927 chr6:30080914-30080926 chr6:30080913-30080927 chr6:30081089-30081102 chr6:30080918-30080926 chr6:30080912-30080927 chr6:30080914-30080926 chr6:30081089-30081102 chr6:30080913-30080925 chr6:30080914-30080926 chr6:30080911-30080929 chr6:30080913-30080926 chr6:30080912-30080927 chr6:30080914-30080927
8	RUNX3	chr6:30080859-30081400	GM12878	blood:	n/a	n/a
9	EP300	chr6:30080801-30081184	HepG2	liver:	n/a	n/a
10	EBF1	chr6:30080865-30081420	GM12878	blood:	n/a	n/a
11	HNF4A	chr6:30080760-30081196	HepG2	liver:	n/a	chr6:30080912-30080927 chr6:30080913-30080927 chr6:30080914-30080926 chr6:30080913-30080927 chr6:30081089-30081102 chr6:30080918-30080926 chr6:30080912-30080927 chr6:30080914-30080926 chr6:30081089-30081102 chr6:30080913-30080925 chr6:30080914-30080926 chr6:30080911-30080929 chr6:30080913-30080926 chr6:30080912-30080927 chr6:30080914-30080927
12	SP1	chr6:30080692-30081239	A549	lung:	n/a	n/a
13	CEBPB	chr6:30080845-30081174	HepG2	liver:	n/a	chr6:30080993-30081004
14	RELA	chr6:30080784-30081392	GM12878	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
15	CEBPB	chr6:30080818-30081177	HepG2	liver:	n/a	chr6:30080993-30081004
16	CEBPB	chr6:30080767-30081257	MCF-7	breast:	n/a	chr6:30080993-30081004
17	RELA	chr6:30080853-30081333	GM12892	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
18	RELA	chr6:30080467-30081547	GM12891	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
19	RELA	chr6:30080848-30081528	GM18505	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
20	RELA	chr6:30080915-30081360	GM18951	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
21	BCL3	chr6:30080840-30081160	A549	lung:	n/a	chr6:30080992-30081001
22	CEBPB	chr6:30080857-30081204	A549	lung:	n/a	chr6:30080993-30081004
23	POU2F2	chr6:30080886-30081271	GM12891	blood:	n/a	chr6:30081085-30081103
24	RELA	chr6:30080879-30081332	GM15510	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
25	EP300	chr6:30080823-30081280	GM12878	blood:	n/a	n/a
26	EBF1	chr6:30080832-30081238	GM12878	blood:	n/a	n/a
27	RELA	chr6:30080827-30081389	GM10847	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
28	EP300	chr6:30080739-30081277	MCF-7	breast:	n/a	chr6:30080761-30080775
29	RCOR1	chr6:30080903-30081098	HepG2	liver:	n/a	n/a
30	ARID3A	chr6:30080773-30081058	HepG2	liver:	n/a	n/a
31	CEBPB	chr6:30080843-30081137	A549	lung:	n/a	chr6:30080993-30081004
32	EBF1	chr6:30080840-30081271	GM12878	blood:	n/a	n/a
33	BATF	chr6:30080814-30081187	GM12878	blood:	n/a	n/a
34	NR2F2	chr6:30080772-30081425	MCF-7	breast:	n/a	chr6:30081045-30081060
35	CEBPB	chr6:30080896-30081087	HepG2	liver:	n/a	chr6:30080993-30081004
36	RELA	chr6:30080820-30081335	GM18526	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30080968-30081018	SK-N-SH_RA	brain:	n/a
2	chr6:30080968-30081018	Hela-S3	cervix:	n/a
3	chr6:30080968-30081018	HCM	heart:	n/a
4	chr6:30080968-30081018	MCF10A-Er-Src	breast:	n/a
5	chr6:30080968-30081018	IMR90	lung:	fetal
6	chr6:30080968-30081018	T-47D	breast:	n/a
7	chr6:30080968-30081018	HNPCEpiC	eye:	n/a
8	chr6:30080968-30081018	K562	blood:	n/a
9	chr6:30080968-30081018	H1-hESC	embryonic stem cell:	embryo
10	chr6:30080968-30081018	GM12878	blood:	n/a
11	chr6:30080968-30081018	HIPEpiC	eye:	n/a
12	chr6:30080968-30081018	AG10803	skin:	n/a
13	chr6:30080968-30081018	HPAEpiC	pulmonary alveolar:	n/a
14	chr6:30080968-30081018	SAEC	small airway:	n/a
15	chr6:30080968-30081018	MCF-7	breast:	n/a
16	chr6:30080968-30081018	AoSMC	blood vessel:	n/a
17	chr6:30080968-30081018	NH-A	brain:	n/a
18	chr6:30080968-30081018	HCT-116	colon:	n/a
19	chr6:30080968-30081018	HCF	heart:	n/a
20	chr6:30080968-30081018	PFSK-1	brain:	n/a
21	chr6:30080968-30081018	HRPEpiC	eye:	n/a
22	chr6:30080968-30081018	GM19239	blood:	n/a
23	chr6:30080968-30081018	GM06990	blood:	n/a
24	chr6:30080968-30081018	HRCEpiC	kidney:	n/a
25	chr6:30080968-30081018	RPTEC	kidney:	n/a
26	chr6:30080968-30081018	AG09309	skin:	n/a
27	chr6:30080968-30081018	AG04450	lung:	fetal
28	chr6:30080968-30081018	U87	brain:	n/a
29	chr6:30080968-30081018	NHDF-neo	bronchial:	n/a
30	chr6:30080968-30081018	HAEpiC	amniotic membrane:	n/a
31	chr6:30080968-30081018	AG09319	gingival:	n/a
32	chr6:30080968-30081018	PrEC	prostate:	n/a
33	chr6:30080968-30081018	HEK293	kidney:	embryo
34	chr6:30080968-30081018	HMEC	breast:	n/a
35	chr6:30080968-30081018	Caco-2	colon:	n/a
36	chr6:30080968-30081018	GM12892	blood:	n/a
37	chr6:30080968-30081018	HepG2	liver:	n/a
38	chr6:30080968-30081018	NT2-D1	testis:	n/a
39	chr6:30080968-30081018	GM12891	blood:	n/a
40	chr6:30080968-30081018	CMK	blood:	n/a
41	chr6:30080968-30081018	AG04449	skin:	fetal
42	chr6:30080968-30081018	A549	lung:	n/a
43	chr6:30080968-30081018	SK-N-SH	brain:	n/a
44	chr6:30080968-30081018	HEEpiC	esophagus:	n/a
45	chr6:30080968-30081018	SK-N-MC	brain:	n/a
46	chr6:30080968-30081018	PANC-1	pancreas:	n/a
47	chr6:30080968-30081018	BJ	skin:	n/a
48	chr6:30080968-30081018	NHBE	bronchial:	n/a
49	chr6:30080968-30081018	NB4	blood:	n/a
50	chr6:30080968-30081018	HRE	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30072138..30074365-chr6:30079433..30082098,2	K562	blood:
2	chr6:30080946..30082589-chr6:30093243..30095341,2	MCF-7	breast:
3	chr6:30072893..30076173-chr6:30078690..30081417,3	MCF-7	breast:

Variant related genes	Relation type
TRIM31	TF binding region
TRIM31	CpG island
ENSG00000231226	Chromatin interaction
ENSG00000204616	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1076229	0.97[ASN][1000 genomes]
rs10947053	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1419671	0.97[ASN][1000 genomes]
rs1419672	0.91[ASN][1000 genomes]
rs1419673	0.99[ASN][1000 genomes]
rs1541324	0.87[ASN][1000 genomes]
rs1573297	0.92[ASN][1000 genomes]
rs1573298	0.82[ASN][1000 genomes]
rs1573299	0.92[ASN][1000 genomes]
rs2284163	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285796	0.86[ASN][1000 genomes]
rs2508030	0.86[ASN][1000 genomes]
rs2508031	0.84[ASN][1000 genomes]
rs2517653	0.83[ASN][1000 genomes]
rs2517655	0.89[ASN][1000 genomes]
rs28400887	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2857433	0.86[ASN][1000 genomes]
rs2857435	0.88[ASN][1000 genomes]
rs2857436	0.82[ASN][1000 genomes]
rs2857438	0.88[ASN][1000 genomes]
rs2857439	0.92[ASN][1000 genomes]
rs2857440	0.88[ASN][1000 genomes]
rs2857458	0.82[ASN][1000 genomes]
rs3815079	0.90[ASN][1000 genomes]
rs3815080	0.82[ASN][1000 genomes]
rs3815082	0.87[ASN][1000 genomes]
rs3815084	0.87[ASN][1000 genomes]
rs3815085	0.87[ASN][1000 genomes]
rs3815086	0.87[ASN][1000 genomes]
rs3888580	0.97[ASN][1000 genomes]
rs4392759	0.92[ASN][1000 genomes]
rs4713293	0.85[ASN][1000 genomes]
rs4959011	0.82[ASN][1000 genomes]
rs4959012	0.92[ASN][1000 genomes]
rs4959041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959044	0.92[ASN][1000 genomes]
rs757259	0.92[ASN][1000 genomes]
rs757261	0.92[ASN][1000 genomes]
rs757262	0.92[ASN][1000 genomes]
rs757263	0.94[ASN][1000 genomes]
rs757264	0.94[ASN][1000 genomes]
rs9261431	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261433	0.99[ASN][1000 genomes]
rs9261438	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261439	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261440	0.96[ASN][1000 genomes]
rs9261442	0.99[ASN][1000 genomes]
rs9261443	0.91[ASN][1000 genomes]
rs9261444	0.99[ASN][1000 genomes]
rs9261445	0.99[ASN][1000 genomes]
rs9261446	0.99[ASN][1000 genomes]
rs9261448	0.95[ASN][1000 genomes]
rs9261449	0.97[ASN][1000 genomes]
rs9261450	0.94[ASN][1000 genomes]
rs9261451	0.94[ASN][1000 genomes]
rs9261453	0.93[ASN][1000 genomes]
rs9261454	0.96[ASN][1000 genomes]
rs9261455	0.93[ASN][1000 genomes]
rs9261456	0.96[ASN][1000 genomes]
rs9261457	0.96[ASN][1000 genomes]
rs9261458	0.96[ASN][1000 genomes]
rs9261459	0.96[ASN][1000 genomes]
rs9261461	0.82[ASN][1000 genomes]
rs9261462	0.92[ASN][1000 genomes]
rs9261463	0.92[ASN][1000 genomes]
rs9261465	0.92[ASN][1000 genomes]
rs9261466	0.88[ASN][1000 genomes]
rs9261467	0.92[ASN][1000 genomes]
rs9261468	0.92[ASN][1000 genomes]
rs9261470	0.88[ASN][1000 genomes]
rs9261471	0.92[ASN][1000 genomes]
rs9261472	0.88[ASN][1000 genomes]
rs9261473	0.92[ASN][1000 genomes]
rs9261479	0.86[ASN][1000 genomes]
rs9261480	0.86[ASN][1000 genomes]
rs9261481	0.82[ASN][1000 genomes]
rs9261482	0.88[ASN][1000 genomes]
rs9261483	0.82[ASN][1000 genomes]
rs9261484	0.82[ASN][1000 genomes]
rs9261485	0.88[ASN][1000 genomes]
rs9261486	0.88[ASN][1000 genomes]
rs9261488	0.92[ASN][1000 genomes]
rs9261489	0.92[ASN][1000 genomes]
rs9261490	0.87[ASN][1000 genomes]
rs9261491	0.87[ASN][1000 genomes]
rs9261492	0.87[ASN][1000 genomes]
rs9261493	0.84[ASN][1000 genomes]
rs9261495	0.92[ASN][1000 genomes]
rs9261496	0.87[ASN][1000 genomes]
rs9261497	0.87[ASN][1000 genomes]
rs9261498	0.82[ASN][1000 genomes]
rs9261499	0.92[ASN][1000 genomes]
rs9261500	0.92[ASN][1000 genomes]
rs9261501	0.87[ASN][1000 genomes]
rs9261502	0.87[ASN][1000 genomes]
rs9261503	0.92[ASN][1000 genomes]
rs9261504	0.88[ASN][1000 genomes]
rs9261505	0.92[ASN][1000 genomes]
rs9261507	0.87[ASN][1000 genomes]
rs9261508	0.87[ASN][1000 genomes]
rs9261509	0.87[ASN][1000 genomes]
rs9261511	0.92[ASN][1000 genomes]
rs9261512	0.89[ASN][1000 genomes]
rs9261513	0.82[ASN][1000 genomes]
rs9261514	0.91[ASN][1000 genomes]
rs9261516	0.89[ASN][1000 genomes]
rs9261517	0.92[ASN][1000 genomes]
rs9261518	0.87[ASN][1000 genomes]
rs9261519	0.87[ASN][1000 genomes]
rs9261521	0.89[ASN][1000 genomes]
rs9261522	0.89[ASN][1000 genomes]
rs9261523	0.87[ASN][1000 genomes]
rs9261524	0.92[ASN][1000 genomes]
rs9261525	0.87[ASN][1000 genomes]
rs9261526	0.86[ASN][1000 genomes]
rs9261527	0.84[ASN][1000 genomes]
rs9261528	0.84[ASN][1000 genomes]
rs9261529	0.86[ASN][1000 genomes]
rs9261530	0.86[ASN][1000 genomes]
rs9261531	0.86[ASN][1000 genomes]
rs9261532	0.86[ASN][1000 genomes]
rs9261533	0.86[ASN][1000 genomes]
rs9261535	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv884055	chr6:30078275-30087776	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9261424	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs9261424	TRIM31	cis	multi-tissue	Pritchard
rs9261424	HCG4P6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30078400-30081400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:30079200-30081000	Active TSS	Colonic Mucosa	Colon
3	chr6:30080000-30081200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
4	chr6:30080000-30081800	Enhancers	Liver	Liver
5	chr6:30080200-30082400	Enhancers	HepG2	liver
6	chr6:30080600-30081000	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr6:30080600-30081000	Enhancers	Hela-S3	cervix
8	chr6:30080600-30081200	Weak transcription	Stomach Mucosa	stomach
9	chr6:30080600-30081800	Flanking Active TSS	GM12878-XiMat	blood
10	chr6:30080800-30081000	Active TSS	Duodenum Mucosa	Duodenum
11	chr6:30080800-30081200	Active TSS	A549	lung
12	chr6:30080800-30081400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr6:30080800-30082800	Enhancers	Fetal Intestine Large	intestine
14	chr6:30080800-30082800	Enhancers	Fetal Intestine Small	intestine

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