Variant report

Variant	rs5753112
Chromosome Location	chr22:30779957-30779958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30713647..30715553-chr22:30779005..30781770,2	MCF-7	breast:
2	chr22:30775755..30777572-chr22:30777818..30782197,3	K562	blood:
3	chr22:30755205..30758055-chr22:30777894..30780330,2	MCF-7	breast:
4	chr22:30768241..30771846-chr22:30779941..30783662,3	MCF-7	breast:
5	chr22:30773208..30775224-chr22:30778192..30780424,2	K562	blood:
6	chr22:30779604..30781335-chr22:30790630..30793179,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099999	Chromatin interaction
ENSG00000100003	Chromatin interaction
ENSG00000099992	Chromatin interaction
ENSG00000241528	Chromatin interaction
ENSG00000187860	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5753112	NIPSNAP1	cis	parietal	SCAN
rs5753112	LOC200312	cis	multi-tissue	Pritchard
rs5753112	SF3A1	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30753200-30782200	Weak transcription	Stomach Mucosa	stomach
2	chr22:30753600-30782000	Weak transcription	Colonic Mucosa	Colon
3	chr22:30753600-30782000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr22:30753600-30782200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr22:30753600-30782400	Weak transcription	Primary T cells from cord blood	blood
6	chr22:30754200-30782000	Weak transcription	Fetal Brain Male	brain
7	chr22:30759600-30782200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr22:30762000-30782400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr22:30764000-30782200	Weak transcription	Right Atrium	heart
10	chr22:30766400-30782200	Weak transcription	Fetal Kidney	kidney
11	chr22:30768600-30781800	Strong transcription	Fetal Stomach	stomach
12	chr22:30769200-30782200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr22:30769200-30782200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr22:30769600-30780400	Strong transcription	Fetal Brain Female	brain
15	chr22:30770200-30781200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr22:30770400-30780600	Strong transcription	Fetal Intestine Small	intestine
17	chr22:30770400-30780800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr22:30771200-30780400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr22:30771200-30780600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr22:30771200-30780600	Strong transcription	Brain Germinal Matrix	brain
21	chr22:30771200-30781000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr22:30771400-30780800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr22:30771600-30780600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr22:30771600-30780800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr22:30772000-30780800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr22:30772000-30783000	Weak transcription	Small Intestine	intestine
27	chr22:30772200-30780800	Strong transcription	Fetal Muscle Leg	muscle
28	chr22:30772200-30782000	Weak transcription	NHDF-Ad	bronchial
29	chr22:30772600-30780400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr22:30772600-30780400	Strong transcription	Placenta	Placenta
31	chr22:30772600-30780800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr22:30772600-30780800	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr22:30772800-30780200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr22:30772800-30780400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr22:30772800-30780400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr22:30773000-30780200	Strong transcription	Brain Cingulate Gyrus	brain
37	chr22:30773000-30780400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr22:30773000-30780400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr22:30773000-30780400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr22:30773000-30780600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr22:30773200-30780800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr22:30773200-30780800	Strong transcription	Lung	lung
43	chr22:30773800-30782200	Weak transcription	HMEC	breast
44	chr22:30774200-30782000	Weak transcription	A549	lung
45	chr22:30774200-30782200	Weak transcription	Brain Substantia Nigra	brain
46	chr22:30774200-30782400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr22:30774200-30782400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr22:30774400-30782400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr22:30775000-30780200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr22:30775000-30780400	Strong transcription	Adipose Nuclei	Adipose

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