Variant report

Variant	rs2120318
Chromosome Location	chr18:9473880-9473881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr18:9473591-9476846	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr18:9473877-9476234	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr18:9473875-9473913	GM12878	blood:	n/a	n/a
4	POLR2A	chr18:9473541-9473912	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9331992..9337338-chr18:9472584..9477624,6	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RALBP1-3	chr18:9473426-9474384	NONHSAT057222
2	lnc-PPP4R1-12	chr18:9473419-9474004	ENSG00000273335.1

No data

Variant related genes	Relation type
RALBP1	TF binding region
ENSG00000264964	Chromatin interaction
ENSG00000128791	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1049553	0.85[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11081480	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs167897	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs329016	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs384178	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389066	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs426897	0.85[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449932	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57315808	0.95[EUR][1000 genomes]
rs59365153	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60376740	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6506672	0.89[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6506673	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7232950	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233044	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7235478	0.85[JPT][hapmap]
rs7235898	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7242756	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7245045	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs72936444	0.80[AMR][1000 genomes];0.94[EUR][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	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2120318	GNAL	cis	cerebellum	SCAN
rs2120318	FAM38B	cis	parietal	SCAN
rs2120318	SPIRE1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9467200-9474200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr18:9470200-9474000	Weak transcription	HUVEC	blood vessel
3	chr18:9473000-9474200	Weak transcription	Thymus	Thymus
4	chr18:9473600-9474000	Enhancers	H9 Cell Line	embryonic stem cell
5	chr18:9473600-9474000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr18:9473600-9474200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr18:9473600-9474200	Enhancers	Brain Germinal Matrix	brain
8	chr18:9473600-9474200	Enhancers	Fetal Heart	heart
9	chr18:9473600-9474200	Enhancers	Fetal Intestine Large	intestine
10	chr18:9473600-9474400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr18:9473800-9474000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr18:9473800-9474000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr18:9473800-9474000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr18:9473800-9474000	Flanking Active TSS	HepG2	liver
15	chr18:9473800-9474200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr18:9473800-9474200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr18:9473800-9474200	Enhancers	Fetal Intestine Small	intestine
18	chr18:9473800-9474200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr18:9473800-9474200	Enhancers	HMEC	breast
20	chr18:9473800-9474200	Enhancers	NHEK	skin
21	chr18:9473800-9474400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr18:9473800-9474400	Enhancers	Fetal Muscle Leg	muscle
23	chr18:9473800-9474400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr18:9473800-9474600	Flanking Active TSS	Fetal Kidney	kidney

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