Variant report

Variant	rs10857580
Chromosome Location	chr10:49686384-49686385
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:49686198..49686718-chr11:62608979..62609573,2	NB4	blood:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10776606	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1077960	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10857577	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10857578	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10857579	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10857582	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11817012	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3888298	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3889332	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3910908	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4080664	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4342982	0.80[ASN][1000 genomes]
rs4838595	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs4838596	0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4838600	0.82[ASN][1000 genomes]
rs7070411	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv467191	chr10:49669142-49735563	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv550813	chr10:49669142-49735563	Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10857580	LRRC18	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49678200-49687200	Weak transcription	HSMMtube	muscle
2	chr10:49679200-49690400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:49679800-49686800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:49679800-49689000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr10:49679800-49704200	Weak transcription	NH-A	brain
6	chr10:49679800-49704200	Weak transcription	NHDF-Ad	bronchial
7	chr10:49681200-49689200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr10:49683200-49687600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr10:49683400-49689200	Strong transcription	NHLF	lung
10	chr10:49683600-49687400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:49683600-49688800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:49683800-49689600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr10:49684000-49686800	Weak transcription	Spleen	Spleen
14	chr10:49684000-49689000	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr10:49684400-49688600	Weak transcription	Right Atrium	heart
16	chr10:49684600-49687000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:49684600-49687400	Strong transcription	HSMM	muscle
18	chr10:49684600-49688000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr10:49684600-49688600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:49684800-49688600	Weak transcription	Left Ventricle	heart
21	chr10:49684800-49690600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr10:49684800-49693000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr10:49685000-49687200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:49685000-49687400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr10:49685000-49689000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr10:49685400-49686400	Enhancers	Brain Substantia Nigra	brain
27	chr10:49685400-49686400	Genic enhancers	Osteobl	bone
28	chr10:49685600-49701000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr10:49685800-49686400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr10:49685800-49687600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:49685800-49687800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr10:49685800-49692000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr10:49685800-49692600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr10:49685800-49694800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr10:49685800-49704800	Weak transcription	HUVEC	blood vessel
36	chr10:49686200-49686600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr10:49686200-49687400	Genic enhancers	K562	blood

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