Variant report

Variant	rs2847277
Chromosome Location	chr18:12778032-12778033
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr18:12778029-12778079	HCF	heart:	n/a
2	chr18:12778029-12778079	MCF10A-Er-Src	breast:	n/a
3	chr18:12778029-12778079	SAEC	small airway:	n/a
4	chr18:12778029-12778079	SK-N-SH	brain:	n/a
5	chr18:12778029-12778079	Jurkat	blood:	n/a
6	chr18:12778029-12778079	BE2_C	brain:	n/a
7	chr18:12778029-12778079	NHDF-neo	bronchial:	n/a
8	chr18:12778029-12778079	HEK293	kidney:	embryo
9	chr18:12778029-12778079	HAEpiC	amniotic membrane:	n/a
10	chr18:12778029-12778079	HCPEpiC	choroid plexus:	n/a
11	chr18:12778029-12778079	GM06990	blood:	n/a
12	chr18:12778029-12778079	HMEC	breast:	n/a
13	chr18:12778029-12778079	AG04450	lung:	fetal
14	chr18:12778029-12778079	AG04449	skin:	fetal
15	chr18:12778029-12778079	LNCaP	prostate:	n/a
16	chr18:12778029-12778079	HL-60	blood:	n/a
17	chr18:12778029-12778079	SK-N-MC	brain:	n/a
18	chr18:12778029-12778079	HIPEpiC	eye:	n/a
19	chr18:12778029-12778079	IMR90	lung:	fetal
20	chr18:12778029-12778079	SKMC	muscle:	n/a
21	chr18:12778029-12778079	AG10803	skin:	n/a
22	chr18:12778029-12778079	HCT-116	colon:	n/a
23	chr18:12778029-12778079	SK-N-SH_RA	brain:	n/a
24	chr18:12778029-12778079	A549	lung:	n/a
25	chr18:12778029-12778079	GM19239	blood:	n/a
26	chr18:12778029-12778079	AG09319	gingival:	n/a
27	chr18:12778029-12778079	HRE	kidney:	n/a
28	chr18:12778029-12778079	HNPCEpiC	eye:	n/a
29	chr18:12778029-12778079	HPAEpiC	pulmonary alveolar:	n/a
30	chr18:12778029-12778079	AG09309	skin:	n/a
31	chr18:12778029-12778079	GM12891	blood:	n/a
32	chr18:12778029-12778079	HepG2	liver:	n/a
33	chr18:12778029-12778079	ProgFib	skin:	n/a
34	chr18:12778029-12778079	NHBE	bronchial:	n/a
35	chr18:12778029-12778079	HRCEpiC	kidney:	n/a
36	chr18:12778029-12778079	AoSMC	blood vessel:	n/a
37	chr18:12778029-12778079	GM12878	blood:	n/a
38	chr18:12778029-12778079	Hela-S3	cervix:	n/a
39	chr18:12778029-12778079	NB4	blood:	n/a
40	chr18:12778029-12778079	RPTEC	kidney:	n/a
41	chr18:12778029-12778079	H1-hESC	embryonic stem cell:	embryo
42	chr18:12778029-12778079	T-47D	breast:	n/a
43	chr18:12778029-12778079	BJ	skin:	n/a
44	chr18:12778029-12778079	GM12892	blood:	n/a
45	chr18:12778029-12778079	HUVEC	blood vessel:	n/a
46	chr18:12778029-12778079	HEEpiC	esophagus:	n/a
47	chr18:12778029-12778079	NH-A	brain:	n/a
48	chr18:12778029-12778079	U87	brain:	n/a
49	chr18:12778029-12778079	ECC-1	luminal epithelium:	n/a
50	chr18:12778029-12778079	ovcar-3	ovarian:	n/a

No data

Variant related genes	Relation type
ENSG00000260302	CpG island

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11663472	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11876290	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2542152	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2542157	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2542160	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542162	0.81[AMR][1000 genomes]
rs2542167	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2847256	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2847257	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2847258	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2847261	0.85[ASN][1000 genomes]
rs2847265	0.83[ASN][1000 genomes]
rs2847276	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847281	0.81[AMR][1000 genomes]
rs2847285	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847286	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847291	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847292	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2847298	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2847299	0.85[ASN][1000 genomes]
rs45456495	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs888269	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs888271	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1062149	chr18:12728115-12783898	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
9	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2847277	RP11-973H7.4	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12767400-12815800	Weak transcription	Gastric	stomach
2	chr18:12776000-12793600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr18:12776200-12785800	Weak transcription	Primary T cells from cord blood	blood
4	chr18:12776200-12791600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr18:12776200-12792600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr18:12776200-12793800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr18:12776200-12793800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr18:12776200-12794000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr18:12776200-12800800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr18:12776400-12800000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr18:12776600-12778200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr18:12776800-12778200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr18:12776800-12788600	Weak transcription	Dnd41	blood
14	chr18:12776800-12819800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr18:12777400-12778200	Active TSS	Fetal Intestine Small	intestine
16	chr18:12777400-12791400	Weak transcription	Left Ventricle	heart
17	chr18:12777600-12788600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr18:12777600-12791800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr18:12777800-12778200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr18:12777800-12785000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr18:12777800-12788600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr18:12777800-12791600	Weak transcription	Primary B cells from cord blood	blood
23	chr18:12777800-12791600	Weak transcription	Liver	Liver
24	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
25	chr18:12778000-12778200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
26	chr18:12778000-12778200	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr18:12778000-12778200	Enhancers	Placenta	Placenta
28	chr18:12778000-12778600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr18:12778000-12778600	Enhancers	Fetal Thymus	thymus
30	chr18:12778000-12782200	Weak transcription	Thymus	Thymus
31	chr18:12778000-12788600	Weak transcription	Lung	lung
32	chr18:12778000-12792800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr18:12778000-12801200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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