Variant report

Variant	rs10491040
Chromosome Location	chr10:49782417-49782418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:49781506..49783468-chr10:49787135..49789633,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDFY4-2	chr10:49782017-49782955	ENSG00000250000

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1015921	0.83[CHD][hapmap]
rs10491041	0.83[CHD][hapmap]
rs10491042	0.83[CHD][hapmap]
rs10776614	0.80[CEU][hapmap];0.86[CHD][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10776615	0.87[CEU][hapmap];0.86[CHD][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10776616	0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10776618	0.83[CHD][hapmap]
rs10857592	0.81[ASN][1000 genomes]
rs10857596	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101362	0.81[ASN][1000 genomes]
rs11101364	0.81[ASN][1000 genomes]
rs11101368	0.81[ASN][1000 genomes]
rs11101377	0.85[ASN][1000 genomes]
rs11101381	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11101382	1.00[CEU][hapmap]
rs11101384	0.87[ASN][1000 genomes]
rs11591281	0.81[ASN][1000 genomes]
rs12358311	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12358315	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12412164	0.85[ASN][1000 genomes]
rs1345104	0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs1345109	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1345110	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1345111	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1445148	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1473323	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1814478	0.83[CHD][hapmap]
rs1838568	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1838569	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1838570	1.00[CEU][hapmap];0.86[CHD][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1838573	0.84[ASN][1000 genomes]
rs1838574	0.86[ASN][1000 genomes]
rs1838576	0.83[CHD][hapmap]
rs1838579	0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs1900021	0.84[ASN][1000 genomes]
rs1965170	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2077152	0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs2120905	0.83[CHD][hapmap]
rs2120910	0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs34983450	0.81[ASN][1000 genomes]
rs4084916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4101278	0.84[ASN][1000 genomes]
rs4101281	0.83[CHD][hapmap]
rs4450130	0.81[ASN][1000 genomes]
rs4838421	0.87[ASN][1000 genomes]
rs4838422	0.87[ASN][1000 genomes]
rs4838617	0.85[ASN][1000 genomes]
rs4838623	0.87[ASN][1000 genomes]
rs4838626	0.83[CHD][hapmap]
rs56058334	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56080723	0.84[ASN][1000 genomes]
rs56248718	0.84[ASN][1000 genomes]
rs57601353	0.81[ASN][1000 genomes]
rs6537568	0.81[ASN][1000 genomes]
rs66695288	0.81[ASN][1000 genomes]
rs67372461	0.81[ASN][1000 genomes]
rs7071095	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7071480	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7074631	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7085183	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7085335	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7087729	1.00[CEU][hapmap]
rs7088010	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7094216	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7096053	0.81[ASN][1000 genomes]
rs7098068	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7350424	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7350439	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7358032	0.83[CHD][hapmap]
rs747533	0.81[ASN][1000 genomes]
rs7894707	0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs7894971	0.87[ASN][1000 genomes]
rs7896644	0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs7904456	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7905247	0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs7916108	0.87[ASN][1000 genomes]
rs935271	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	nsv550815	chr10:49774633-49794481	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv550816	chr10:49782417-49794481	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10491040	A1CF	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49773000-49782600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr10:49773000-49787400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr10:49773200-49787800	Weak transcription	Brain Angular Gyrus	brain
4	chr10:49773400-49786200	Weak transcription	Brain Hippocampus Middle	brain
5	chr10:49773400-49786600	Strong transcription	HSMM	muscle
6	chr10:49775600-49782600	Weak transcription	Aorta	Aorta
7	chr10:49776400-49786200	Weak transcription	Brain Substantia Nigra	brain
8	chr10:49777000-49787400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr10:49777400-49787400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr10:49778800-49783800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr10:49779000-49782600	Enhancers	Primary B cells from peripheral blood	blood
12	chr10:49779000-49782600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr10:49779200-49784400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr10:49779400-49788000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr10:49780200-49783600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:49780200-49783800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:49780400-49782800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr10:49780800-49787200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr10:49781000-49782600	Weak transcription	HUVEC	blood vessel
20	chr10:49781200-49786000	Strong transcription	Osteobl	bone
21	chr10:49781200-49786200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:49781200-49786800	Strong transcription	NH-A	brain
23	chr10:49781200-49787000	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr10:49781600-49782600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr10:49781600-49783000	Strong transcription	HMEC	breast
26	chr10:49781600-49783800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:49782000-49783200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr10:49782200-49782600	Enhancers	Primary B cells from cord blood	blood
29	chr10:49782200-49783000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr10:49782200-49783000	Strong transcription	HSMMtube	muscle
31	chr10:49782200-49786200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr10:49782400-49783200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr10:49782400-49783200	Flanking Active TSS	GM12878-XiMat	blood
34	chr10:49782400-49783800	Strong transcription	NHDF-Ad	bronchial
35	chr10:49782400-49784200	Strong transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links