Variant report

Variant	rs12660945
Chromosome Location	chr6:71669874-71669875
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr6:71669592-71669908	SH-SY5Y	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:71669827-71669877	HRE	kidney:	n/a
2	chr6:71669827-71669877	HEEpiC	esophagus:	n/a
3	chr6:71669827-71669877	T-47D	breast:	n/a
4	chr6:71669827-71669877	PrEC	prostate:	n/a
5	chr6:71669827-71669877	A549	lung:	n/a
6	chr6:71669827-71669877	GM06990	blood:	n/a
7	chr6:71669827-71669877	NB4	blood:	n/a
8	chr6:71669827-71669877	HMEC	breast:	n/a
9	chr6:71669827-71669877	NHDF-neo	bronchial:	n/a
10	chr6:71669827-71669877	MCF10A-Er-Src	breast:	n/a
11	chr6:71669827-71669877	K562	blood:	n/a
12	chr6:71669827-71669877	BJ	skin:	n/a
13	chr6:71669827-71669877	PANC-1	pancreas:	n/a
14	chr6:71669827-71669877	HL-60	blood:	n/a
15	chr6:71669827-71669877	IMR90	lung:	fetal
16	chr6:71669827-71669877	AG09319	gingival:	n/a
17	chr6:71669827-71669877	Hela-S3	cervix:	n/a
18	chr6:71669827-71669877	Hepatocyte	liver:	n/a
19	chr6:71669827-71669877	PFSK-1	brain:	n/a
20	chr6:71669827-71669877	MCF-7	breast:	n/a
21	chr6:71669827-71669877	SKMC	muscle:	n/a
22	chr6:71669827-71669877	NHBE	bronchial:	n/a
23	chr6:71669827-71669877	SAEC	small airway:	n/a
24	chr6:71669827-71669877	HPAEpiC	pulmonary alveolar:	n/a
25	chr6:71669827-71669877	BE2_C	brain:	n/a
26	chr6:71669827-71669877	Jurkat	blood:	n/a
27	chr6:71669827-71669877	HCT-116	colon:	n/a
28	chr6:71669827-71669877	SK-N-SH	brain:	n/a
29	chr6:71669827-71669877	AG04449	skin:	fetal
30	chr6:71669827-71669877	GM12891	blood:	n/a
31	chr6:71669827-71669877	SK-N-MC	brain:	n/a
32	chr6:71669827-71669877	GM12878	blood:	n/a
33	chr6:71669827-71669877	U87	brain:	n/a
34	chr6:71669827-71669877	ProgFib	skin:	n/a
35	chr6:71669827-71669877	ovcar-3	ovarian:	n/a
36	chr6:71669827-71669877	HCPEpiC	choroid plexus:	n/a
37	chr6:71669827-71669877	HIPEpiC	eye:	n/a
38	chr6:71669827-71669877	SK-N-SH_RA	brain:	n/a
39	chr6:71669827-71669877	HepG2	liver:	n/a
40	chr6:71669827-71669877	HCM	heart:	n/a
41	chr6:71669827-71669877	HCF	heart:	n/a
42	chr6:71669827-71669877	HRCEpiC	kidney:	n/a
43	chr6:71669827-71669877	H1-hESC	embryonic stem cell:	embryo
44	chr6:71669827-71669877	AoSMC	blood vessel:	n/a
45	chr6:71669827-71669877	HUVEC	blood vessel:	n/a
46	chr6:71669827-71669877	HRPEpiC	eye:	n/a
47	chr6:71669827-71669877	GM12892	blood:	n/a
48	chr6:71669827-71669877	AG10803	skin:	n/a
49	chr6:71669827-71669877	LNCaP	prostate:	n/a
50	chr6:71669827-71669877	HEK293	kidney:	embryo

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:71665737..71667966-chr6:71669230..71671989,2	K562	blood:
2	chr6:71660383..71662410-chr6:71669635..71671756,2	K562	blood:

No data

Variant related genes	Relation type
B3GAT2	TF binding region
B3GAT2	CpG island
ENSG00000112309	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10455717	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1111994	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504740	0.89[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	nsv886148	chr6:71623253-71694742	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links