Variant report

Variant	rs11800996
Chromosome Location	chr1:85413380-85413381
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	chr1:85412729..85414874-chr1:85716251..85718921,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10873667	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808352	0.82[CEU][hapmap]
rs17117919	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs58279485	1.00[EUR][1000 genomes]
rs58977145	1.00[EUR][1000 genomes]
rs653213	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs72944567	0.84[EUR][1000 genomes]
rs72944579	0.97[EUR][1000 genomes]
rs72944587	1.00[EUR][1000 genomes]
rs72944593	1.00[EUR][1000 genomes]
rs72944595	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74098721	0.89[EUR][1000 genomes]
rs7545349	0.82[CEU][hapmap]

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
rs11800996	MCOLN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 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	chr1:85410600-85413400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr1:85411200-85413800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:85411200-85414200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:85411200-85414200	Enhancers	NHEK	skin
7	chr1:85411200-85414600	Weak transcription	Brain Substantia Nigra	brain
8	chr1:85411400-85414200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:85411400-85416400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:85411400-85426200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:85411600-85414400	Genic enhancers	GM12878-XiMat	blood
12	chr1:85411800-85416200	Weak transcription	Primary B cells from cord blood	blood
13	chr1:85412000-85415200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:85412000-85415600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:85412000-85424600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:85412000-85425200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:85412200-85415400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:85412200-85430200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:85413000-85413800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr1:85413000-85413800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:85413000-85413800	Enhancers	Esophagus	oesophagus
22	chr1:85413000-85414000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:85413000-85414200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:85413000-85414200	Enhancers	Dnd41	blood
25	chr1:85413000-85414200	Enhancers	HMEC	breast
26	chr1:85413200-85413400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr1:85413200-85413800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:85413200-85414000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:85413200-85416800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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