Variant report

Variant	rs570564
Chromosome Location	chr1:85413765-85413766
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	chr1:85412729..85414874-chr1:85716251..85718921,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12118848	0.86[GIH][hapmap]
rs12124346	0.82[EUR][1000 genomes]
rs12138367	0.82[TSI][hapmap]
rs12145036	0.86[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1325277	0.84[CHB][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs589332	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs621003	0.98[ASN][1000 genomes]
rs639500	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs650357	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs666779	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][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
rs570564	MCOLN2	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85402000-85419600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:85410400-85413800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:85411200-85413800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:85411200-85414200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:85411200-85414200	Enhancers	NHEK	skin
6	chr1:85411200-85414600	Weak transcription	Brain Substantia Nigra	brain
7	chr1:85411400-85414200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:85411400-85416400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:85411400-85426200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:85411600-85414400	Genic enhancers	GM12878-XiMat	blood
11	chr1:85411800-85416200	Weak transcription	Primary B cells from cord blood	blood
12	chr1:85412000-85415200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:85412000-85415600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:85412000-85424600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:85412000-85425200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:85412200-85415400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:85412200-85430200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:85413000-85413800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr1:85413000-85413800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:85413000-85413800	Enhancers	Esophagus	oesophagus
21	chr1:85413000-85414000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:85413000-85414200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:85413000-85414200	Enhancers	Dnd41	blood
24	chr1:85413000-85414200	Enhancers	HMEC	breast
25	chr1:85413200-85413800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:85413200-85414000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:85413200-85416800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:85413400-85413800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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