Variant report

Variant	rs58977145
Chromosome Location	chr1:85410242-85410243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:85410006..85410936-chr1:85495368..85495874,2	MCF-7	breast:
2	chr1:84382101..84384733-chr1:85409125..85411327,2	K562	blood:
3	chr1:85410240..85410751-chr1:85493199..85493798,2	MCF-7	breast:
4	chr1:85409879..85410688-chr1:85705752..85706654,2	K562	blood:
5	chr1:85410128..85411315-chr1:85490122..85491874,8	MCF-7	breast:
6	chr1:85410118..85411009-chr1:85725007..85725639,2	MCF-7	breast:
7	chr1:85410065..85411348-chr1:85724616..85726527,9	K562	blood:
8	chr1:85409622..85411011-chr1:85492995..85494617,8	MCF-7	breast:
9	chr1:85410011..85410751-chr1:85491092..85491875,2	MCF-7	breast:
10	chr1:85410009..85411013-chr1:85724647..85725830,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162642	Chromatin interaction
ENSG00000055732	Chromatin interaction

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]
rs58279485	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs653213	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72944567	0.84[EUR][1000 genomes]
rs72944579	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72944587	0.91[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
rs58977145	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 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	chr1:85400800-85410800	Weak transcription	Fetal Lung	lung
4	chr1:85402000-85410400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:85402000-85419600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:85402200-85410400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:85403800-85410800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:85405000-85413200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:85405200-85413000	Weak transcription	Esophagus	oesophagus
10	chr1:85405800-85410400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:85406600-85410400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:85406600-85410800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:85406600-85410800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:85406600-85410800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:85406800-85410400	Weak transcription	NHEK	skin
16	chr1:85406800-85410800	Weak transcription	HMEC	breast
17	chr1:85406800-85412000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:85410200-85410400	Enhancers	Stomach Mucosa	stomach
19	chr1:85410200-85410600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:85410200-85410600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr1:85410200-85410600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:85410200-85410600	Enhancers	Dnd41	blood
23	chr1:85410200-85410600	Enhancers	GM12878-XiMat	blood
24	chr1:85410200-85410800	Enhancers	Primary B cells from peripheral blood	blood
25	chr1:85410200-85410800	Enhancers	Fetal Thymus	thymus

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