Variant report

Variant	rs1108957
Chromosome Location	chr13:51822346-51822347
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	chr13:51820571..51823207-chr13:51824938..51826606,2	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1108958	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12584566	0.93[CHB][hapmap];0.90[CHD][hapmap]
rs2408302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3990078	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942984	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1108957	VPS36	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51805200-51825600	Weak transcription	Aorta	Aorta
2	chr13:51813200-51822600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:51816200-51836600	Weak transcription	Adipose Nuclei	Adipose
4	chr13:51816800-51836000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr13:51817400-51827200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr13:51817600-51827200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr13:51817800-51827600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:51818800-51832800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr13:51820200-51822400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:51820200-51823800	Genic enhancers	H1 Cell Line	embryonic stem cell
11	chr13:51820200-51825000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:51820600-51823000	Genic enhancers	H9 Cell Line	embryonic stem cell
13	chr13:51820800-51833000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:51821000-51824200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
15	chr13:51821200-51822400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr13:51821200-51823000	Enhancers	Colon Smooth Muscle	Colon
17	chr13:51821200-51824600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr13:51821200-51829600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:51821400-51823800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr13:51821400-51824800	Weak transcription	Lung	lung
21	chr13:51821400-51824800	Weak transcription	Right Ventricle	heart
22	chr13:51821400-51825600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr13:51821400-51825800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr13:51821400-51825800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr13:51821400-51825800	Weak transcription	Left Ventricle	heart
26	chr13:51821400-51827200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr13:51821400-51829600	Weak transcription	Right Atrium	heart
28	chr13:51821400-51833200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr13:51821400-51833800	Weak transcription	Gastric	stomach
30	chr13:51821600-51822400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr13:51821600-51822400	Enhancers	Brain Hippocampus Middle	brain
32	chr13:51821600-51822400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr13:51821600-51822400	Weak transcription	Fetal Brain Female	brain
34	chr13:51821600-51823000	Enhancers	Brain Angular Gyrus	brain
35	chr13:51821600-51825400	Enhancers	Brain Cingulate Gyrus	brain
36	chr13:51821600-51836200	Weak transcription	Fetal Muscle Leg	muscle
37	chr13:51821600-51839000	Weak transcription	Esophagus	oesophagus
38	chr13:51821600-51845000	Weak transcription	Fetal Brain Male	brain
39	chr13:51821800-51822400	Weak transcription	Brain Germinal Matrix	brain
40	chr13:51821800-51822600	Weak transcription	Pancreas	Pancrea
41	chr13:51821800-51822800	Enhancers	Stomach Smooth Muscle	stomach
42	chr13:51821800-51825000	Weak transcription	Fetal Stomach	stomach
43	chr13:51821800-51825200	Enhancers	Brain Anterior Caudate	brain
44	chr13:51821800-51825400	Enhancers	Brain Substantia Nigra	brain
45	chr13:51821800-51825600	Weak transcription	Spleen	Spleen
46	chr13:51821800-51825800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr13:51821800-51831400	Weak transcription	Fetal Lung	lung
48	chr13:51822000-51822400	Enhancers	Fetal Heart	heart
49	chr13:51822000-51822800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
50	chr13:51822000-51823400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell

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