Variant report

Variant	rs2523976
Chromosome Location	chr6:30084696-30084697
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:30084620-30084770	HCM	heart:	n/a	n/a
2	CTCF	chr6:30084560-30084710	AoAF	blood vessel:	n/a	n/a
3	CTCF	chr6:30084680-30084830	GM12864	blood:	n/a	n/a
4	CTCF	chr6:30084600-30084750	AG10803	skin:	n/a	n/a
5	CTCF	chr6:30084640-30084790	GM12864	blood:	n/a	n/a
6	CTCF	chr6:30084600-30084750	HMEC	breast:	n/a	n/a
7	CTCF	chr6:30084560-30084710	HVMF	connective:	n/a	n/a
8	CTCF	chr6:30084600-30084750	AG09319	gingival:	n/a	n/a
9	CTCF	chr6:30084680-30084830	HMF	breast:	n/a	n/a
10	CTCF	chr6:30084660-30084810	HCT-116	colon:	n/a	n/a
11	CTCF	chr6:30084660-30084810	HPAF	blood vessel:	n/a	n/a
12	CTCF	chr6:30084600-30084750	AG04450	lung:	n/a	n/a
13	CTCF	chr6:30084660-30084810	HL-60	blood:	n/a	n/a
14	CTCF	chr6:30084640-30084790	HCPEpiC	choroid plexus:	n/a	n/a
15	CTCF	chr6:30084580-30084730	HCT-116	colon:	n/a	n/a
16	CTCF	chr6:30084680-30084830	BJ	skin:	n/a	n/a
17	CTCF	chr6:30084620-30084770	AoAF	blood vessel:	n/a	n/a
18	CTCF	chr6:30084680-30084830	SK-N-SH_RA	brain:	n/a	n/a
19	CTCF	chr6:30084580-30084730	SAEC	small airway:	n/a	n/a
20	CTCF	chr6:30084680-30084830	AG04449	skin:	n/a	n/a
21	CTCF	chr6:30084620-30084770	HCFaa	heart:	n/a	n/a
22	CTCF	chr6:30084660-30084810	GM12865	blood:	n/a	n/a
23	CTCF	chr6:30084660-30084810	GM12872	blood:	n/a	n/a
24	CTCF	chr6:30084640-30084790	AG04449	skin:	n/a	n/a
25	CTCF	chr6:30084620-30084770	AG10803	skin:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30083851..30086480-chr6:30123012..30125789,2	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM31	TF binding region

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]
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]
rs2844792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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
rs2523976	HLA-C	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30082000-30089400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:30082200-30086400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:30082200-30087400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:30082400-30087200	Weak transcription	Hela-S3	cervix
5	chr6:30082400-30091000	Weak transcription	HepG2	liver
6	chr6:30082600-30086400	Weak transcription	Stomach Mucosa	stomach
7	chr6:30082600-30086400	Weak transcription	A549	lung
8	chr6:30082800-30086200	Weak transcription	Fetal Intestine Large	intestine
9	chr6:30082800-30086200	Weak transcription	Fetal Intestine Small	intestine

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