Variant report

Variant	rs3780622
Chromosome Location	chr9:101763633-101763634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101760174..101763909-chr9:101764160..101767138,3	K562	blood:
2	chr9:101762797..101765082-chr9:101923950..101926109,2	MCF-7	breast:
3	chr9:101759295..101764429-chr9:101866150..101870418,5	K562	blood:

Variant related genes	Relation type
ENSG00000106799	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10988521	0.87[JPT][hapmap]
rs10988530	0.82[JPT][hapmap]
rs12378396	0.83[JPT][hapmap]
rs55687154	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043134	0.91[JPT][hapmap]

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	nsv6635	chr9:101728257-101773253	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3780622	C9orf3	cis	cerebellum	SCAN
rs3780622	CDC14B	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101760200-101772800	Weak transcription	Aorta	Aorta
2	chr9:101760400-101767400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:101761200-101763800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:101761600-101767400	Weak transcription	Colonic Mucosa	Colon
5	chr9:101761600-101768400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:101761600-101770400	Weak transcription	Fetal Intestine Small	intestine
7	chr9:101761600-101814400	Weak transcription	Gastric	stomach
8	chr9:101761800-101764000	Weak transcription	Hela-S3	cervix
9	chr9:101761800-101765200	Weak transcription	Fetal Stomach	stomach
10	chr9:101761800-101765400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:101761800-101765400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:101761800-101765600	Weak transcription	Left Ventricle	heart
13	chr9:101761800-101765800	Weak transcription	Ovary	ovary
14	chr9:101761800-101765800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:101761800-101768200	Weak transcription	Spleen	Spleen
16	chr9:101761800-101777800	Weak transcription	Pancreas	Pancrea
17	chr9:101761800-101785200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:101762400-101764200	Weak transcription	NHLF	lung
19	chr9:101762600-101764000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:101762600-101764000	Genic enhancers	Placenta	Placenta
21	chr9:101762600-101769400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr9:101762800-101763800	Enhancers	Thymus	Thymus
23	chr9:101762800-101763800	Enhancers	HSMM	muscle
24	chr9:101762800-101764000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr9:101762800-101764000	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr9:101762800-101764000	Genic enhancers	Fetal Muscle Leg	muscle
27	chr9:101762800-101764200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr9:101762800-101764200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:101762800-101764200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr9:101762800-101764200	Genic enhancers	Adipose Nuclei	Adipose
31	chr9:101762800-101764400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:101762800-101764600	Enhancers	K562	blood
33	chr9:101762800-101765400	Enhancers	Primary T cells from cord blood	blood
34	chr9:101762800-101765400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:101762800-101769000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr9:101762800-101769600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr9:101763000-101763800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:101763000-101763800	Enhancers	Brain Hippocampus Middle	brain
39	chr9:101763000-101764000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr9:101763000-101764400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr9:101763000-101764600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:101763000-101764600	Enhancers	Fetal Thymus	thymus
43	chr9:101763000-101764800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:101763000-101764800	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr9:101763000-101764800	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr9:101763000-101765000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr9:101763000-101765000	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr9:101763000-101765000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr9:101763000-101765200	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr9:101763000-101765400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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