Variant report

Variant	rs72953098
Chromosome Location	chr3:118864997-118864998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:183)
Chromatin interactive
region (count:1)
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	POLR2A	chr3:118864677-118865020	MCF-7	breast:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:118864974-118865024	RPTEC	kidney:	n/a
2	chr3:118864952-118865002	BE2_C	brain:	n/a
3	chr3:118864974-118865024	GM12892	blood:	n/a
4	chr3:118864952-118865002	HRPEpiC	eye:	n/a
5	chr3:118864966-118865016	GM19239	blood:	n/a
6	chr3:118864974-118865024	AG09319	gingival:	n/a
7	chr3:118864966-118865016	Caco-2	colon:	n/a
8	chr3:118864974-118865024	BE2_C	brain:	n/a
9	chr3:118864952-118865002	HepG2	liver:	n/a
10	chr3:118864966-118865016	HCF	heart:	n/a
11	chr3:118864966-118865016	AG04449	skin:	fetal
12	chr3:118864974-118865024	GM06990	blood:	n/a
13	chr3:118864966-118865016	MCF10A-Er-Src	breast:	n/a
14	chr3:118864966-118865016	GM12878	blood:	n/a
15	chr3:118864966-118865016	HL-60	blood:	n/a
16	chr3:118864974-118865024	AoSMC	blood vessel:	n/a
17	chr3:118864952-118865002	HRE	kidney:	n/a
18	chr3:118864966-118865016	MCF-7	breast:	n/a
19	chr3:118864966-118865016	HRE	kidney:	n/a
20	chr3:118864966-118865016	ovcar-3	ovarian:	n/a
21	chr3:118864952-118865002	K562	blood:	n/a
22	chr3:118864966-118865016	SK-N-SH_RA	brain:	n/a
23	chr3:118864952-118865002	HAEpiC	amniotic membrane:	n/a
24	chr3:118864952-118865002	NHDF-neo	bronchial:	n/a
25	chr3:118864952-118865002	HCF	heart:	n/a
26	chr3:118864966-118865016	HCT-116	colon:	n/a
27	chr3:118864952-118865002	Hepatocyte	liver:	n/a
28	chr3:118864966-118865016	BJ	skin:	n/a
29	chr3:118864952-118865002	HRCEpiC	kidney:	n/a
30	chr3:118864974-118865024	PFSK-1	brain:	n/a
31	chr3:118864952-118865002	Caco-2	colon:	n/a
32	chr3:118864966-118865016	AG09319	gingival:	n/a
33	chr3:118864974-118865024	AG09309	skin:	n/a
34	chr3:118864952-118865002	HNPCEpiC	eye:	n/a
35	chr3:118864974-118865024	HUVEC	blood vessel:	n/a
36	chr3:118864952-118865002	T-47D	breast:	n/a
37	chr3:118864974-118865024	HPAEpiC	pulmonary alveolar:	n/a
38	chr3:118864974-118865024	SAEC	small airway:	n/a
39	chr3:118864952-118865002	HIPEpiC	eye:	n/a
40	chr3:118864952-118865002	HCPEpiC	choroid plexus:	n/a
41	chr3:118864974-118865024	AG04450	lung:	fetal
42	chr3:118864974-118865024	ECC-1	luminal epithelium:	n/a
43	chr3:118864952-118865002	HCM	heart:	n/a
44	chr3:118864952-118865002	HL-60	blood:	n/a
45	chr3:118864952-118865002	Hela-S3	cervix:	n/a
46	chr3:118864974-118865024	T-47D	breast:	n/a
47	chr3:118864966-118865016	PANC-1	pancreas:	n/a
48	chr3:118864966-118865016	NH-A	brain:	n/a
49	chr3:118864952-118865002	ovcar-3	ovarian:	n/a
50	chr3:118864952-118865002	GM06990	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:118863527..118866220-chr3:118958408..118962544,4	MCF-7	breast:

No data

Variant related genes	Relation type
C3orf30	TF binding region
IGSF11	TF binding region
ENSG00000251012	TF binding region
IGSF11	CpG island
ENSG00000251012	CpG island
C3orf30	CpG island
ENSG00000121578	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12489443	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490484	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493435	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12493755	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1369576	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35784102	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56048248	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56337924	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57299098	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58432707	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61101462	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61672117	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773865	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6775604	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775750	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792069	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792705	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793572	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808358	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72953077	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72953092	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72953094	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955008	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955012	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955015	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72955025	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73854414	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615519	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616863	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7629056	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630771	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633391	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829692	chr3:118727772-118901711	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118863800-118865200	Enhancers	A549	lung
2	chr3:118864400-118865000	Enhancers	Placenta	Placenta
3	chr3:118864400-118865000	Enhancers	K562	blood
4	chr3:118864600-118865200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:118864600-118865200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:118864600-118865600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:118864800-118867200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:118864800-118867200	Weak transcription	Gastric	stomach
9	chr3:118864800-118867400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:118864800-118867400	Weak transcription	HMEC	breast
11	chr3:118864800-118870000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:118864800-118874800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links