Variant report

Variant	rs1860528
Chromosome Location	chr2:235009685-235009686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs60069251	1.00[AMR][1000 genomes]
rs73996531	1.00[AMR][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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv834571	chr2:234929288-235110332	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv998149	chr2:234978261-235086951	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1008675	chr2:235002241-235021724	Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1860528	SYCE1	trans	lymphoblastoid	seeQTL
rs1860528	ARL4C	cis	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:235002400-235010000	Weak transcription	Pancreas	Pancrea
2	chr2:235006800-235011600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:235007000-235010800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:235007600-235011400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr2:235007600-235011400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr2:235007800-235010000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:235007800-235010200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:235007800-235011200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr2:235007800-235011400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:235007800-235011400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:235007800-235011400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:235007800-235011600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:235008000-235009800	Weak transcription	Fetal Thymus	thymus
14	chr2:235009400-235009800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr2:235009600-235010000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:235009600-235010000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:235009600-235010000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr2:235009600-235010200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr2:235009600-235010200	Flanking Active TSS	Dnd41	blood
20	chr2:235009600-235010800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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