Variant report

Variant	rs10890313
Chromosome Location	chr1:45175925-45175926
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45175330..45177217-chr1:45283598..45286133,2	K562	blood:
2	chr1:45171369..45177382-chr1:45282549..45286855,7	K562	blood:
3	chr1:45174154..45176275-chr1:45267387..45269114,2	K562	blood:
4	chr1:45166407..45168535-chr1:45174409..45176231,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198520	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11211024	0.90[MEX][hapmap];0.82[MKK][hapmap]
rs11211025	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211026	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211036	0.93[CEU][hapmap]
rs11211038	0.92[CEU][hapmap]
rs11211040	0.93[CEU][hapmap]
rs11211053	0.86[CEU][hapmap]
rs1140279	0.87[CEU][hapmap]
rs11573562	0.93[CEU][hapmap]
rs11580159	0.84[EUR][1000 genomes]
rs11584440	0.93[CEU][hapmap]
rs11800505	0.88[EUR][1000 genomes]
rs11803622	0.93[CEU][hapmap];0.89[TSI][hapmap]
rs12139143	0.93[CEU][hapmap]
rs12732939	0.92[CEU][hapmap]
rs12733586	0.93[CEU][hapmap]
rs12735728	0.85[EUR][1000 genomes]
rs12746270	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs12746898	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16832227	0.93[CEU][hapmap]
rs16832263	0.93[CEU][hapmap]
rs17881698	0.93[CEU][hapmap]
rs17883049	0.93[CEU][hapmap]
rs2295997	0.92[CEU][hapmap]
rs3795714	0.93[CEU][hapmap]
rs3795719	0.93[CEU][hapmap]
rs3820586	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs4342887	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs6429550	0.93[CEU][hapmap]
rs6676749	0.93[CEU][hapmap]
rs6689911	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs6692487	0.93[CEU][hapmap]
rs6702415	0.80[EUR][1000 genomes]
rs6703452	0.93[CEU][hapmap]
rs7517439	0.93[CEU][hapmap]
rs7517639	0.93[CEU][hapmap]
rs7534487	0.93[CEU][hapmap]
rs7546285	0.93[CEU][hapmap]

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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
5	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
6	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10890313	SNORD55	cis	parietal	SCAN
rs10890313	EIF2B3	cis	cerebellum	SCAN
rs10890313	SNORD38B	cis	cerebellum	SCAN
rs10890313	UROD	cis	multi-tissue	Pritchard
rs10890313	TIE1	cis	parietal	SCAN
rs10890313	SNORD55	cis	cerebellum	SCAN
rs10890313	BEST4	cis	lymphoblastoid	seeQTL
rs10890313	ZNF642	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45169200-45180600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:45172200-45180600	Weak transcription	Right Atrium	heart
3	chr1:45174000-45178200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:45174000-45179000	Weak transcription	Hela-S3	cervix
5	chr1:45174000-45180400	Weak transcription	Brain Substantia Nigra	brain
6	chr1:45174200-45178000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:45174200-45179400	Weak transcription	Small Intestine	intestine
8	chr1:45174200-45180600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:45174400-45177400	Weak transcription	Primary B cells from cord blood	blood
10	chr1:45174400-45177400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:45174400-45178200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:45174400-45178600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:45174400-45179200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:45174400-45180600	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:45174400-45180800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:45174400-45183000	Weak transcription	NHLF	lung
17	chr1:45174400-45190400	Weak transcription	Lung	lung
18	chr1:45174600-45179000	Weak transcription	HMEC	breast
19	chr1:45174600-45179000	Weak transcription	NHEK	skin
20	chr1:45174600-45180600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:45174600-45180600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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