Variant report

Variant	rs2844792
Chromosome Location	chr6:30080956-30080957
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	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.	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
ENSG00000204616	Chromatin interaction
ENSG00000231226	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1034326	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1034327	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541269	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2239529	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2245420	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2249099	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2427749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517598	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523981	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523982	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523983	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523984	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523985	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523989	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523992	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2844790	0.93[EUR][1000 genomes]
rs2844791	0.81[EUR][1000 genomes]
rs2844793	0.87[EUR][1000 genomes];0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2844792	HLA-C	Cis_chr	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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