Variant report

Variant	rs2847298
Chromosome Location	chr18:12800120-12800121
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11663472	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11876290	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12971201	0.87[YRI][hapmap]
rs2542152	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2542157	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2542160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542162	0.83[CEU][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs2542167	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2847256	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2847257	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847258	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2847276	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2847277	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2847281	0.83[CEU][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs2847285	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2847286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2847291	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2847292	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2847299	0.93[ASN][1000 genomes]
rs45456495	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478582	0.87[YRI][hapmap]
rs4797709	1.00[YRI][hapmap]
rs674222	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs8087237	0.87[YRI][hapmap]
rs888269	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs888271	0.93[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
8	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
rs2847298	RP11-973H7.4	cis	Whole Blood	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12767400-12815800	Weak transcription	Gastric	stomach
2	chr18:12776200-12800800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr18:12776800-12819800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
5	chr18:12778000-12801200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:12782000-12811200	Weak transcription	Right Ventricle	heart
7	chr18:12784400-12801200	Weak transcription	Fetal Intestine Small	intestine
8	chr18:12784600-12809000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr18:12785000-12803600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr18:12787400-12808800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr18:12787600-12815800	Weak transcription	Pancreas	Pancrea
12	chr18:12788400-12802000	Weak transcription	Colon Smooth Muscle	Colon
13	chr18:12789000-12802600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr18:12789000-12821400	Weak transcription	Small Intestine	intestine
15	chr18:12789200-12814200	Weak transcription	Fetal Kidney	kidney
16	chr18:12789600-12808800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr18:12789800-12809000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr18:12789800-12809000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr18:12790200-12828000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr18:12790400-12809000	Weak transcription	HSMM	muscle
21	chr18:12790400-12813600	Weak transcription	A549	lung
22	chr18:12790400-12814000	Weak transcription	Osteobl	bone
23	chr18:12790400-12815800	Weak transcription	K562	blood
24	chr18:12790600-12820000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr18:12791200-12815800	Weak transcription	Brain Germinal Matrix	brain
26	chr18:12791200-12819600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr18:12791400-12819600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr18:12791400-12837000	Weak transcription	NHDF-Ad	bronchial
29	chr18:12791600-12802800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr18:12791600-12828000	Weak transcription	HUVEC	blood vessel
31	chr18:12791800-12803000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr18:12791800-12821600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr18:12792200-12800400	Strong transcription	Primary T cells from cord blood	blood
34	chr18:12792200-12815800	Weak transcription	NH-A	brain
35	chr18:12792800-12802600	Weak transcription	Fetal Brain Male	brain
36	chr18:12792800-12802800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr18:12792800-12815800	Weak transcription	Brain Angular Gyrus	brain
38	chr18:12792800-12819600	Weak transcription	NHLF	lung
39	chr18:12793000-12802200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr18:12793000-12811400	Strong transcription	Fetal Thymus	thymus
41	chr18:12794400-12806400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr18:12794600-12800800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr18:12794600-12800800	Weak transcription	Brain Hippocampus Middle	brain
44	chr18:12794600-12801200	Weak transcription	Ovary	ovary
45	chr18:12794600-12802600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr18:12794600-12803000	Weak transcription	Hela-S3	cervix
47	chr18:12794600-12809000	Weak transcription	HSMMtube	muscle
48	chr18:12794600-12815800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr18:12794800-12809000	Weak transcription	Aorta	Aorta
50	chr18:12795000-12801200	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links