Variant report

Variant	rs1841499
Chromosome Location	chr1:72836456-72836457
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10789336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209948	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11209951	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11209952	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584611	0.81[CHB][hapmap]
rs1380995	0.81[CHB][hapmap]
rs1432639	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1460942	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1460943	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1776012	0.81[CHB][hapmap]
rs2568958	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs2568960	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568961	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2613494	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815752	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815753	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3101336	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs3101340	0.81[CHB][hapmap]
rs9424977	0.81[CHB][hapmap]
rs990871	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv428454	chr1:72504469-72926256	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	esv2757734	chr1:72742396-72886813	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2758939	chr1:72742396-72886813	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3491557	chr1:72742853-72851634	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3491558	chr1:72742853-72851634	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv830204	chr1:72749851-72938571	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3584809	chr1:72768936-72844844	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
8	nsv947113	chr1:72810737-72948614	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv2422432	chr1:72821856-73148651	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1841499	RP11-292O17.1	cis	Thyroid	GTEx
rs1841499	RP11-292O17.1	cis	Nerve Tibial	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72832400-72836800	Weak transcription	HMEC	breast
2	chr1:72832400-72837000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:72832800-72837200	Weak transcription	NHEK	skin
4	chr1:72832800-72837400	Weak transcription	Hela-S3	cervix
5	chr1:72833200-72837400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:72834800-72837800	Enhancers	Dnd41	blood
7	chr1:72835000-72837000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:72835400-72837200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:72835600-72837000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:72835600-72840000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:72836200-72837600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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