Variant report

Variant	rs12345407
Chromosome Location	chr9:108474538-108474539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:108474522-108475476	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108456301..108459785-chr9:108473235..108475830,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228366	TF binding region
ENSG00000095209	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs16924820	1.00[EUR][1000 genomes]
rs16924997	0.83[EUR][1000 genomes]
rs34006675	1.00[EUR][1000 genomes]
rs35232724	1.00[EUR][1000 genomes]
rs57288965	1.00[EUR][1000 genomes]
rs57544538	1.00[EUR][1000 genomes]
rs57694909	1.00[EUR][1000 genomes]
rs58554531	1.00[EUR][1000 genomes]
rs58943241	1.00[EUR][1000 genomes]
rs59314159	1.00[EUR][1000 genomes]
rs59747314	1.00[EUR][1000 genomes]
rs6477452	1.00[EUR][1000 genomes]
rs7030040	1.00[EUR][1000 genomes]
rs7047325	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs73516084	0.83[EUR][1000 genomes]
rs73518117	1.00[EUR][1000 genomes]
rs73518124	1.00[EUR][1000 genomes]
rs73518141	1.00[EUR][1000 genomes]
rs73518160	1.00[EUR][1000 genomes]
rs73518170	1.00[EUR][1000 genomes]
rs73518183	1.00[EUR][1000 genomes]
rs73520071	1.00[EUR][1000 genomes]
rs73520092	1.00[EUR][1000 genomes]
rs73520094	1.00[EUR][1000 genomes]
rs73522007	1.00[EUR][1000 genomes]
rs73522022	1.00[EUR][1000 genomes]
rs73522055	1.00[EUR][1000 genomes]
rs73522056	1.00[EUR][1000 genomes]
rs73522061	1.00[EUR][1000 genomes]
rs73522067	1.00[EUR][1000 genomes]
rs7866807	1.00[EUR][1000 genomes]
rs7870562	1.00[EUR][1000 genomes]
rs7873482	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv615116	chr9:108468129-108546438	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12345407	SPIN1	trans	brain	seeQTL
rs12345407	OXR1	trans	brain	seeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108457800-108476200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:108457800-108492200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:108458000-108475200	Weak transcription	Fetal Thymus	thymus
4	chr9:108458000-108475600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:108458000-108475600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:108458000-108475600	Weak transcription	Thymus	Thymus
7	chr9:108458000-108476000	Weak transcription	Ovary	ovary
8	chr9:108458000-108479200	Weak transcription	Fetal Brain Male	brain
9	chr9:108458000-108497800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:108458200-108476400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:108458200-108478800	Weak transcription	Brain Hippocampus Middle	brain
12	chr9:108458200-108480800	Weak transcription	Brain Angular Gyrus	brain
13	chr9:108458200-108491400	Weak transcription	HSMMtube	muscle
14	chr9:108458200-108491600	Weak transcription	Brain Anterior Caudate	brain
15	chr9:108458200-108495400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:108458200-108497000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:108459000-108476000	Weak transcription	Fetal Brain Female	brain
18	chr9:108459200-108489400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:108463200-108478400	Weak transcription	Hela-S3	cervix
20	chr9:108463200-108496800	Weak transcription	HepG2	liver
21	chr9:108463400-108487600	Weak transcription	Primary B cells from cord blood	blood
22	chr9:108464000-108474800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:108464200-108474800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr9:108464400-108476000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:108465000-108496600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr9:108465600-108476200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:108466200-108476200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr9:108466800-108478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr9:108468400-108475000	Weak transcription	Right Ventricle	heart
30	chr9:108468800-108475400	Weak transcription	Fetal Stomach	stomach
31	chr9:108469000-108476200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr9:108469000-108485000	Weak transcription	Small Intestine	intestine
33	chr9:108469200-108475000	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:108469200-108476000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:108469200-108478000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:108469800-108476400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:108470600-108476000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr9:108470600-108497000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr9:108470800-108474600	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr9:108470800-108487200	Weak transcription	Liver	Liver
41	chr9:108470800-108496000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr9:108471000-108476400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:108471000-108495400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr9:108471200-108481600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr9:108471400-108475600	Weak transcription	Fetal Intestine Large	intestine
46	chr9:108471400-108477600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:108471400-108479200	Weak transcription	Esophagus	oesophagus
48	chr9:108471600-108475800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:108472000-108476600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:108472200-108476400	Weak transcription	Brain Substantia Nigra	brain

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