Variant report

Variant	rs58279485
Chromosome Location	chr1:85406998-85406999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85405508..85407651-chr1:85733535..85736514,2	K562	blood:
2	chr1:85405603..85407474-chr1:85407528..85409146,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10873667	1.00[EUR][1000 genomes]
rs11800996	1.00[EUR][1000 genomes]
rs17117919	1.00[EUR][1000 genomes]
rs58977145	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs653213	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72944567	0.84[EUR][1000 genomes]
rs72944579	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72944587	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72944593	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72944595	1.00[EUR][1000 genomes]
rs74098721	0.89[EUR][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	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58279485	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85396400-85410600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:85396600-85410800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:85399000-85410000	Strong transcription	GM12878-XiMat	blood
4	chr1:85400800-85410800	Weak transcription	Fetal Lung	lung
5	chr1:85402000-85410400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:85402000-85419600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:85402200-85410200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:85402200-85410400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:85403800-85410800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:85404600-85408000	Weak transcription	Spleen	Spleen
11	chr1:85405000-85413200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:85405200-85413000	Weak transcription	Esophagus	oesophagus
13	chr1:85405800-85410400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr1:85406600-85410400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:85406600-85410800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:85406600-85410800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:85406600-85410800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:85406800-85410400	Weak transcription	NHEK	skin
19	chr1:85406800-85410800	Weak transcription	HMEC	breast
20	chr1:85406800-85412000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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