Variant report

Variant	rs11855110
Chromosome Location	chr15:52372521-52372522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:52372420-52372570	HMEC	breast:	n/a	n/a
2	CTCF	chr15:52372480-52372630	SAEC	small airway:	n/a	n/a
3	E2F4	chr15:52372323-52372523	MCF10A-Er-Src	breast:	n/a	n/a
4	CTCF	chr15:52372380-52372530	HEEpiC	esophagus:	n/a	n/a
5	STAT3	chr15:52372275-52372569	MCF10A-Er-Src	breast:	n/a	n/a
6	EBF1	chr15:52372354-52372695	GM12878	blood:	n/a	chr15:52372502-52372513 chr15:52372527-52372538
7	STAT3	chr15:52371907-52372582	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr15:52372303-52372522	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr15:52372235-52372598	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr15:52372235-52372607	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr15:52372281-52372571	MCF10A-Er-Src	breast:	n/a	n/a
12	CTCF	chr15:52372400-52372550	HRPEpiC	eye:	n/a	n/a
13	POLR2A	chr15:52372256-52372524	H1-neurons	neurons:	n/a	n/a
14	FOS	chr15:52372255-52372612	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr15:52372275-52372592	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr15:52372180-52372667	MCF10A-Er-Src	breast:	n/a	n/a
17	MYC	chr15:52372288-52372598	MCF10A-Er-Src	breast:	n/a	n/a
18	CTCF	chr15:52372480-52372630	HMEC	breast:	n/a	n/a
19	STAT3	chr15:52372242-52372575	MCF10A-Er-Src	breast:	n/a	n/a
20	CTCF	chr15:52372420-52372570	NHEK	skin:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52262830..52265268-chr15:52372078..52374982,4	MCF-7	breast:
2	chr15:52309334..52315760-chr15:52366746..52373412,20	MCF-7	breast:
3	chr15:52339947..52342319-chr15:52368984..52372783,3	MCF-7	breast:
4	chr15:52274293..52274815-chr15:52372080..52373063,2	MCF-7	breast:
5	chr15:52371404..52373055-chr15:52373147..52374878,2	MCF-7	breast:
6	chr15:52263873..52266562-chr15:52369853..52372558,3	MCF-7	breast:
7	chr15:52362758..52365823-chr15:52370997..52373206,3	K562	blood:
8	chr15:52362758..52364447-chr15:52370997..52373206,2	K562	blood:
9	chr15:52355832..52357497-chr15:52369964..52372920,2	MCF-7	breast:
10	chr15:52370736..52372537-chr15:52471693..52473323,2	MCF-7	breast:
11	chr15:52308069..52314807-chr15:52359242..52376066,34	MCF-7	breast:
12	chr15:52371333..52373042-chr15:52391102..52393252,2	MCF-7	breast:
13	chr15:52267047..52268763-chr15:52371441..52374035,2	K562	blood:
14	chr15:52371710..52374413-chr15:52385596..52389516,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAPK6-13	chr15:52372326-52372524	NONHSAT043908

No data

Variant related genes	Relation type
ENSG00000259178	TF binding region
ENSG00000069956	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000259178	Chromatin interaction
ENSG00000259712	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000242327	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11854569	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28501427	0.88[EUR][1000 genomes]
rs28718531	0.90[EUR][1000 genomes]
rs56049741	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56186119	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62015205	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62015208	0.89[EUR][1000 genomes]
rs9672817	0.89[EUR][1000 genomes]
rs9672830	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats 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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1039841	chr15:52357448-52381377	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11855110	SCG3	cis	Cerebellum	GTEx
rs11855110	SCG3	cis	Temporal Cortex	GTEx
rs11855110	SCG3	cis	Frontal Cortex	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52357600-52373200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:52362800-52374600	Weak transcription	Small Intestine	intestine
3	chr15:52364600-52374000	Weak transcription	Pancreas	Pancrea
4	chr15:52367600-52373200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:52369600-52373000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:52369800-52373400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:52369800-52373400	Enhancers	HMEC	breast
8	chr15:52369800-52374400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:52369800-52374400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:52369800-52374400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr15:52369800-52374400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr15:52370000-52372800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:52370000-52374400	Weak transcription	HSMMtube	muscle
14	chr15:52370600-52373000	Enhancers	NHEK	skin
15	chr15:52370800-52374600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr15:52370800-52376400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:52371200-52374400	Weak transcription	Brain Anterior Caudate	brain
18	chr15:52371200-52374400	Weak transcription	Colonic Mucosa	Colon
19	chr15:52371200-52374400	Weak transcription	Esophagus	oesophagus
20	chr15:52371200-52374400	Weak transcription	Dnd41	blood
21	chr15:52371200-52374800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:52371200-52376600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:52371400-52374000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr15:52371400-52374400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:52371400-52377400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:52371600-52373000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:52371600-52378800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr15:52371800-52374000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:52371800-52374600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:52372000-52372600	Enhancers	GM12878-XiMat	blood

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