Variant report

Variant	rs2023473
Chromosome Location	chr6:30075613-30075614
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:4)
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	FOS	chr6:30075602-30075878	MCF10A-Er-Src	breast:	n/a	chr6:30075743-30075752
2	FOS	chr6:30075550-30075876	MCF10A-Er-Src	breast:	n/a	chr6:30075743-30075752
3	FOS	chr6:30075595-30075795	MCF10A-Er-Src	breast:	n/a	chr6:30075743-30075752
4	FOS	chr6:30075602-30075874	MCF10A-Er-Src	breast:	n/a	chr6:30075743-30075752

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30075605-30075655	PANC-1	pancreas:	n/a
2	chr6:30075605-30075655	HCPEpiC	choroid plexus:	n/a
3	chr6:30075605-30075655	GM12891	blood:	n/a
4	chr6:30075605-30075655	GM06990	blood:	n/a
5	chr6:30075605-30075655	HIPEpiC	eye:	n/a
6	chr6:30075605-30075655	Caco-2	colon:	n/a
7	chr6:30075605-30075655	A549	lung:	n/a
8	chr6:30075605-30075655	BE2_C	brain:	n/a
9	chr6:30075605-30075655	NT2-D1	testis:	n/a
10	chr6:30075605-30075655	AG04449	skin:	fetal
11	chr6:30075605-30075655	SK-N-MC	brain:	n/a
12	chr6:30075605-30075655	HCM	heart:	n/a
13	chr6:30075605-30075655	ECC-1	luminal epithelium:	n/a
14	chr6:30075605-30075655	MCF10A-Er-Src	breast:	n/a
15	chr6:30075605-30075655	SAEC	small airway:	n/a
16	chr6:30075605-30075655	T-47D	breast:	n/a
17	chr6:30075605-30075655	PFSK-1	brain:	n/a
18	chr6:30075605-30075655	PrEC	prostate:	n/a
19	chr6:30075605-30075655	BJ	skin:	n/a
20	chr6:30075605-30075655	HRPEpiC	eye:	n/a
21	chr6:30075605-30075655	HL-60	blood:	n/a
22	chr6:30075605-30075655	NH-A	brain:	n/a
23	chr6:30075605-30075655	HPAEpiC	pulmonary alveolar:	n/a
24	chr6:30075605-30075655	HCF	heart:	n/a
25	chr6:30075605-30075655	K562	blood:	n/a
26	chr6:30075605-30075655	Hela-S3	cervix:	n/a
27	chr6:30075605-30075655	AG09309	skin:	n/a
28	chr6:30075605-30075655	IMR90	lung:	fetal
29	chr6:30075605-30075655	HepG2	liver:	n/a
30	chr6:30075605-30075655	HAEpiC	amniotic membrane:	n/a
31	chr6:30075605-30075655	GM12878	blood:	n/a
32	chr6:30075605-30075655	HUVEC	blood vessel:	n/a
33	chr6:30075605-30075655	LNCaP	prostate:	n/a
34	chr6:30075605-30075655	Jurkat	blood:	n/a
35	chr6:30075605-30075655	RPTEC	kidney:	n/a
36	chr6:30075605-30075655	AG04450	lung:	fetal
37	chr6:30075605-30075655	GM12892	blood:	n/a
38	chr6:30075605-30075655	HMEC	breast:	n/a
39	chr6:30075605-30075655	ovcar-3	ovarian:	n/a
40	chr6:30075605-30075655	AG09319	gingival:	n/a
41	chr6:30075605-30075655	ProgFib	skin:	n/a
42	chr6:30075605-30075655	Hepatocyte	liver:	n/a
43	chr6:30075605-30075655	HRE	kidney:	n/a
44	chr6:30075605-30075655	SK-N-SH_RA	brain:	n/a
45	chr6:30075605-30075655	AoSMC	blood vessel:	n/a
46	chr6:30075605-30075655	H1-hESC	embryonic stem cell:	embryo
47	chr6:30075605-30075655	NB4	blood:	n/a
48	chr6:30075605-30075655	NHDF-neo	bronchial:	n/a
49	chr6:30075605-30075655	GM19239	blood:	n/a
50	chr6:30075605-30075655	SK-N-SH	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr6:30071292..30074099-chr6:30075439..30077084,2	K562	blood:
2	chr6:30028230..30030474-chr6:30075345..30077234,2	MCF-7	breast:
3	chr6:30072893..30076173-chr6:30078690..30081417,3	MCF-7	breast:
4	chr6:30073473..30076763-chr6:30077230..30080756,3	K562	blood:

No data

Variant related genes	Relation type
TRIM31	TF binding region
TRIM31	CpG island
ENSG00000231226	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000204616	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11158	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1264705	0.90[EUR][1000 genomes]
rs1264706	0.90[EUR][1000 genomes]
rs1573296	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1970	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2106072	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2157678	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2517601	0.90[EUR][1000 genomes]
rs2517609	0.85[EUR][1000 genomes]
rs2517617	0.85[EUR][1000 genomes]
rs2517622	0.91[EUR][1000 genomes]
rs2523712	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2523729	0.91[EUR][1000 genomes]
rs2523978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2844777	0.81[EUR][1000 genomes]
rs2844789	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3094146	0.80[EUR][1000 genomes]
rs3115631	0.85[EUR][1000 genomes]
rs8321	0.88[EUR][1000 genomes]
rs9261290	0.86[EUR][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	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2023473	HLA-C	Cis_chr	lymphoblastoid	RTeQTL
rs2023473	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2023473	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30071600-30079200	Weak transcription	Gastric	stomach
2	chr6:30072200-30078000	Weak transcription	Colonic Mucosa	Colon
3	chr6:30073600-30075800	Strong transcription	Fetal Intestine Small	intestine
4	chr6:30074400-30076600	Weak transcription	Stomach Mucosa	stomach
5	chr6:30075200-30076000	Enhancers	Hela-S3	cervix
6	chr6:30075400-30075800	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr6:30075400-30075800	Strong transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links