Variant report

Variant	rs6478262
Chromosome Location	chr9:100319280-100319281
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	chr9:100319150..100321068-chr9:100324699..100328167,3	K562	blood:
2	chr9:100318639..100320970-chr9:100327548..100329985,2	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10982745	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2094758	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7037608	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7871185	0.99[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	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6478262	TMOD1	cis	cerebellum	SCAN
rs6478262	C9orf130	cis	parietal	SCAN
rs6478262	GALNT12	cis	parietal	SCAN
rs6478262	C9orf156	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100306800-100321000	Weak transcription	HSMMtube	muscle
2	chr9:100308200-100319400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:100308200-100319600	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:100310000-100319400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:100311600-100319400	Weak transcription	GM12878-XiMat	blood
6	chr9:100311800-100325200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:100315600-100326200	Weak transcription	Esophagus	oesophagus
8	chr9:100316000-100322400	Enhancers	Right Atrium	heart
9	chr9:100316400-100322400	Enhancers	Left Ventricle	heart
10	chr9:100316600-100322400	Enhancers	Ovary	ovary
11	chr9:100317000-100320000	Enhancers	Pancreas	Pancrea
12	chr9:100317000-100320200	Enhancers	Aorta	Aorta
13	chr9:100317200-100321400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr9:100317200-100322000	Enhancers	Fetal Brain Male	brain
15	chr9:100317600-100319800	Enhancers	Brain Anterior Caudate	brain
16	chr9:100317600-100321000	Enhancers	Brain Hippocampus Middle	brain
17	chr9:100317600-100321600	Enhancers	Brain Cingulate Gyrus	brain
18	chr9:100317800-100319600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr9:100317800-100321200	Weak transcription	K562	blood
20	chr9:100318000-100321000	Enhancers	Brain Angular Gyrus	brain
21	chr9:100318000-100321800	Enhancers	Fetal Heart	heart
22	chr9:100318200-100319400	Genic enhancers	Stomach Smooth Muscle	stomach
23	chr9:100318200-100320200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:100318200-100321800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:100318200-100322400	Enhancers	Right Ventricle	heart
26	chr9:100318400-100320000	Enhancers	Gastric	stomach
27	chr9:100318400-100321000	Enhancers	Liver	Liver
28	chr9:100318600-100319600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:100318600-100321400	Enhancers	Psoas Muscle	Psoas
30	chr9:100318800-100320200	Enhancers	Stomach Mucosa	stomach
31	chr9:100318800-100320600	Enhancers	Fetal Brain Female	brain
32	chr9:100318800-100323200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:100319000-100319600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr9:100319000-100319600	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr9:100319000-100319800	Enhancers	Adipose Nuclei	Adipose
36	chr9:100319000-100320000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:100319000-100320000	Enhancers	Brain Substantia Nigra	brain
38	chr9:100319000-100321400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr9:100319200-100319800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr9:100319200-100320000	Enhancers	Placenta	Placenta
41	chr9:100319200-100320200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:100319200-100320200	Enhancers	Lung	lung
43	chr9:100319200-100320400	Enhancers	H9 Cell Line	embryonic stem cell
44	chr9:100319200-100320600	Enhancers	Spleen	Spleen
45	chr9:100319200-100327400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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