Variant report

Variant	rs17749547
Chromosome Location	chr6:54710440-54710441
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:54710340-54713314	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr6:54710248-54714679	MCF-7	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:54710399-54710449	GM12891	blood:	n/a
2	chr6:54710399-54710449	HMEC	breast:	n/a
3	chr6:54710399-54710449	HCM	heart:	n/a
4	chr6:54710399-54710449	SAEC	small airway:	n/a
5	chr6:54710399-54710449	PrEC	prostate:	n/a
6	chr6:54710399-54710449	HRE	kidney:	n/a
7	chr6:54710399-54710449	GM12892	blood:	n/a
8	chr6:54710399-54710449	T-47D	breast:	n/a
9	chr6:54710399-54710449	RPTEC	kidney:	n/a
10	chr6:54710399-54710449	HPAEpiC	pulmonary alveolar:	n/a
11	chr6:54710399-54710449	Caco-2	colon:	n/a
12	chr6:54710399-54710449	HCT-116	colon:	n/a
13	chr6:54710399-54710449	AG09309	skin:	n/a
14	chr6:54710399-54710449	HRCEpiC	kidney:	n/a
15	chr6:54710399-54710449	NHDF-neo	bronchial:	n/a
16	chr6:54710399-54710449	AG04450	lung:	fetal
17	chr6:54710399-54710449	NT2-D1	testis:	n/a
18	chr6:54710399-54710449	AG04449	skin:	fetal
19	chr6:54710399-54710449	K562	blood:	n/a
20	chr6:54710399-54710449	GM06990	blood:	n/a
21	chr6:54710399-54710449	Hepatocyte	liver:	n/a
22	chr6:54710399-54710449	HL-60	blood:	n/a
23	chr6:54710399-54710449	AG10803	skin:	n/a
24	chr6:54710399-54710449	H1-hESC	embryonic stem cell:	embryo
25	chr6:54710399-54710449	ProgFib	skin:	n/a
26	chr6:54710399-54710449	PANC-1	pancreas:	n/a
27	chr6:54710399-54710449	IMR90	lung:	fetal
28	chr6:54710399-54710449	CMK	blood:	n/a
29	chr6:54710399-54710449	SKMC	muscle:	n/a
30	chr6:54710399-54710449	Jurkat	blood:	n/a
31	chr6:54710399-54710449	NHBE	bronchial:	n/a
32	chr6:54710399-54710449	ECC-1	luminal epithelium:	n/a
33	chr6:54710399-54710449	PFSK-1	brain:	n/a
34	chr6:54710399-54710449	HIPEpiC	eye:	n/a
35	chr6:54710399-54710449	MCF10A-Er-Src	breast:	n/a
36	chr6:54710399-54710449	HCPEpiC	choroid plexus:	n/a
37	chr6:54710399-54710449	BE2_C	brain:	n/a
38	chr6:54710399-54710449	HEK293	kidney:	embryo
39	chr6:54710399-54710449	NH-A	brain:	n/a
40	chr6:54710399-54710449	GM19239	blood:	n/a
41	chr6:54710399-54710449	SK-N-MC	brain:	n/a
42	chr6:54710399-54710449	HNPCEpiC	eye:	n/a
43	chr6:54710399-54710449	AoSMC	blood vessel:	n/a
44	chr6:54710399-54710449	ovcar-3	ovarian:	n/a
45	chr6:54710399-54710449	HCF	heart:	n/a
46	chr6:54710399-54710449	HEEpiC	esophagus:	n/a
47	chr6:54710399-54710449	SK-N-SH_RA	brain:	n/a
48	chr6:54710399-54710449	BJ	skin:	n/a
49	chr6:54710399-54710449	HRPEpiC	eye:	n/a
50	chr6:54710399-54710449	MCF-7	breast:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:54483454..54486448-chr6:54709404..54710933,2	MCF-7	breast:
2	chr6:54709139..54711220-chr6:54750997..54752618,2	MCF-7	breast:
3	chr6:54556132..54558033-chr6:54708676..54711461,2	MCF-7	breast:
4	chr14:65876592..65878564-chr6:54710365..54711981,2	MCF-7	breast:
5	chr6:54709202..54711186-chr6:54779955..54782595,2	MCF-7	breast:
6	chr6:54633061..54636995-chr6:54710354..54713223,5	MCF-7	breast:

No data

Variant related genes	Relation type
FAM83B	TF binding region
ENSG00000224984	TF binding region
FAM83B	CpG island
ENSG00000224984	CpG island
ENSG00000220635	Chromatin interaction
ENSG00000033170	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12664791	0.96[EUR][1000 genomes]
rs17682328	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17682340	0.92[EUR][1000 genomes]
rs62412606	0.96[EUR][1000 genomes]
rs62412628	0.96[EUR][1000 genomes]
rs62412629	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62412630	0.96[EUR][1000 genomes]
rs62412631	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62412632	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62412635	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62412645	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62412646	0.92[EUR][1000 genomes]
rs62412648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412649	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9357819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396000	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54707200-54710800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:54707400-54710800	Weak transcription	Placenta	Placenta
3	chr6:54709000-54713400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:54709000-54714200	Active TSS	Duodenum Mucosa	Duodenum
5	chr6:54709400-54710800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:54709800-54713400	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr6:54710000-54710600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:54710200-54710800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:54710200-54711200	Flanking Active TSS	HMEC	breast
10	chr6:54710200-54711600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:54710400-54710600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:54710400-54710600	Enhancers	Stomach Mucosa	stomach
13	chr6:54710400-54710800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:54710400-54710800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:54710400-54710800	Enhancers	Hela-S3	cervix
16	chr6:54710400-54711200	Flanking Active TSS	NHEK	skin
17	chr6:54710400-54713200	Active TSS	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links