Variant report

Variant	rs638578
Chromosome Location	chr18:9625750-9625751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11081489	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1662885	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1787165	0.90[ASN][1000 genomes]
rs1787166	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2028661	0.89[ASN][1000 genomes]
rs2028662	0.89[ASN][1000 genomes]
rs2028663	0.89[ASN][1000 genomes]
rs2289684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2903504	0.87[EUR][1000 genomes]
rs328995	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs329002	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329004	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs329023	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs329024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35444634	0.89[ASN][1000 genomes]
rs407530	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs428598	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs583306	0.89[ASN][1000 genomes]
rs586544	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs589559	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs599861	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs610564	0.91[EUR][1000 genomes]
rs62088919	0.84[AMR][1000 genomes]
rs62088920	0.90[ASN][1000 genomes]
rs633907	0.85[CHB][hapmap]
rs667695	0.89[ASN][1000 genomes]
rs671339	0.89[ASN][1000 genomes]
rs677461	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs680478	0.89[ASN][1000 genomes]
rs681297	0.89[ASN][1000 genomes]
rs683319	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs694861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233160	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7234128	1.00[ASN][1000 genomes]
rs8090919	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807577	0.81[ASN][1000 genomes]
rs9807604	0.89[ASN][1000 genomes]
rs9807610	0.86[ASN][1000 genomes]
rs9950583	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	33 gene(s)	inside rSNPs	diseases
3	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv576449	chr18:9623052-9700382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3383704	chr18:9625712-9627822	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs638578	RP11-692N5.1	cis	Nerve Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9615800-9627400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr18:9617600-9630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:9619800-9627400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr18:9620000-9627200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr18:9620000-9627400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr18:9620000-9627600	Weak transcription	NHDF-Ad	bronchial
7	chr18:9620200-9627000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr18:9620200-9627400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr18:9620200-9627400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr18:9620200-9627400	Weak transcription	NHLF	lung
11	chr18:9620200-9627400	Weak transcription	Osteobl	bone
12	chr18:9620800-9627600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr18:9625200-9626400	Enhancers	Placenta	Placenta
14	chr18:9625200-9628200	Enhancers	NHEK	skin
15	chr18:9625400-9625800	Enhancers	HMEC	breast
16	chr18:9625400-9626200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr18:9625400-9626200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr18:9625400-9626400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr18:9625600-9625800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr18:9625600-9626000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr18:9625600-9628200	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links