Variant report

Variant	rs10513467
Chromosome Location	chr3:154749792-154749793
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11923608	1.00[ASN][1000 genomes]
rs16824527	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16824533	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs16824536	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16824540	0.83[AMR][1000 genomes]
rs17442246	0.83[AMR][1000 genomes]
rs1836912	1.00[CEU][hapmap]
rs34860880	0.83[AMR][1000 genomes]
rs34876701	1.00[EUR][1000 genomes]
rs35848304	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773906	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4414805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55862533	0.83[AMR][1000 genomes]
rs55954373	1.00[ASN][1000 genomes]
rs56072333	1.00[ASN][1000 genomes]
rs56317942	0.83[AMR][1000 genomes]
rs56380855	0.83[AMR][1000 genomes]
rs57022891	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57231033	1.00[ASN][1000 genomes]
rs58120007	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58662380	1.00[ASN][1000 genomes]
rs60197267	1.00[ASN][1000 genomes]
rs60351120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60435073	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60948062	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60995161	1.00[ASN][1000 genomes]
rs61064256	1.00[ASN][1000 genomes]
rs61281054	1.00[ASN][1000 genomes]
rs61489236	1.00[ASN][1000 genomes]
rs61761163	0.87[ASN][1000 genomes]
rs6770028	1.00[ASN][1000 genomes]
rs6799870	1.00[ASN][1000 genomes]
rs73874449	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73874454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73874461	1.00[ASN][1000 genomes]
rs73874463	1.00[ASN][1000 genomes]
rs73874467	1.00[ASN][1000 genomes]
rs73874471	1.00[ASN][1000 genomes]
rs73874473	1.00[ASN][1000 genomes]
rs73874476	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73874478	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73874479	1.00[ASN][1000 genomes]
rs73874486	1.00[ASN][1000 genomes]
rs73874488	1.00[ASN][1000 genomes]
rs73874489	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73874493	1.00[ASN][1000 genomes]
rs73874497	1.00[ASN][1000 genomes]
rs7632185	1.00[ASN][1000 genomes]
rs7643334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917791	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9917802	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868930	chr3:154076125-154820242	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1000140	chr3:154336261-154905740	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv534289	chr3:154535584-154987166	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv532663	chr3:154561578-154960353	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10513467	C18orf54	trans	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:154744400-154750200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:154745400-154750400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:154745400-154750400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:154745600-154750400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:154746400-154750400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:154746400-154753400	Weak transcription	K562	blood
7	chr3:154748200-154752800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:154748400-154750600	Enhancers	Adipose Nuclei	Adipose
9	chr3:154748400-154751400	Enhancers	Osteobl	bone
10	chr3:154748400-154752600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:154748400-154753800	Enhancers	NHDF-Ad	bronchial
12	chr3:154748600-154750800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:154748800-154750400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:154749000-154750200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:154749000-154750200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:154749000-154750200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr3:154749000-154750200	Weak transcription	NHLF	lung
18	chr3:154749000-154750400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:154749000-154750600	Weak transcription	HSMMtube	muscle
20	chr3:154749200-154750200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:154749200-154750400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:154749400-154750000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:154749400-154750400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:154749400-154750400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:154749400-154750600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:154749400-154751600	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr3:154749600-154750000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:154749600-154750000	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links