Variant report

Variant	rs439156
Chromosome Location	chr5:118322042-118322043
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118320682..118322479-chr5:118322824..118324515,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169570	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2442119	0.92[AMR][1000 genomes]
rs2442122	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6894429	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs7736118	0.93[AMR][1000 genomes];0.87[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	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1017548	chr5:118276479-118358394	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv969271	chr5:118317943-118323256	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs439156	SNCAIP	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118305200-118322400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:118309600-118323000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr5:118311400-118322800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:118313000-118323000	Weak transcription	Fetal Heart	heart
5	chr5:118313600-118322200	Weak transcription	Primary B cells from cord blood	blood
6	chr5:118314000-118322400	Weak transcription	Primary T cells from cord blood	blood
7	chr5:118314600-118322400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr5:118314600-118323000	Weak transcription	Brain Angular Gyrus	brain
9	chr5:118314600-118323400	Weak transcription	Aorta	Aorta
10	chr5:118315600-118322800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:118315600-118322800	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:118316000-118323000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr5:118316000-118323200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:118316200-118323000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:118316200-118323200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr5:118316200-118323400	Weak transcription	Ovary	ovary
17	chr5:118316200-118323800	Weak transcription	Gastric	stomach
18	chr5:118316800-118323000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:118318800-118323000	Weak transcription	Fetal Intestine Small	intestine
20	chr5:118319000-118323000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:118319200-118323200	Weak transcription	Fetal Thymus	thymus
22	chr5:118320000-118323800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:118320200-118322400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:118320600-118323000	Weak transcription	A549	lung
25	chr5:118321000-118322400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:118321000-118322800	Weak transcription	HMEC	breast
27	chr5:118321000-118322800	Weak transcription	NHEK	skin
28	chr5:118321000-118323000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:118321000-118323000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:118321000-118323000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:118321000-118323000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:118321000-118323000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:118321000-118323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:118321000-118323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:118321000-118323000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:118321000-118323000	Weak transcription	Adipose Nuclei	Adipose
37	chr5:118321000-118323000	Weak transcription	Brain Anterior Caudate	brain
38	chr5:118321000-118323000	Weak transcription	NH-A	brain
39	chr5:118321000-118323200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:118321000-118323200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:118321000-118323200	Weak transcription	Osteobl	bone
42	chr5:118321000-118323400	Weak transcription	HSMMtube	muscle
43	chr5:118321000-118323400	Weak transcription	NHLF	lung
44	chr5:118321200-118323200	Weak transcription	NHDF-Ad	bronchial
45	chr5:118321400-118323000	Enhancers	Dnd41	blood
46	chr5:118321400-118323000	Enhancers	Hela-S3	cervix
47	chr5:118321600-118322800	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr5:118321800-118322800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr5:118321800-118323200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr5:118322000-118322200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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