Variant report

Variant	rs3739799
Chromosome Location	chr9:101784777-101784778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101782641..101786481-chr9:101865510..101868655,3	MCF-7	breast:
2	chr9:101782750..101786222-chr9:101835622..101838699,3	K562	blood:
3	chr9:101782750..101786222-chr9:101834554..101837470,3	K562	blood:
4	chr9:101774409..101777052-chr9:101782515..101785003,2	K562	blood:
5	chr9:101782923..101785154-chr9:101866625..101868401,2	K562	blood:
6	chr9:101783791..101786672-chr9:101794290..101796962,2	K562	blood:
7	chr9:101767464..101769714-chr9:101783800..101785964,2	MCF-7	breast:
8	chr9:101783186..101785549-chr9:101797018..101799423,2	K562	blood:
9	chr9:101780306..101785966-chr9:101786034..101790764,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000106799	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10988510	0.82[JPT][hapmap]
rs10988521	0.87[JPT][hapmap];0.83[MKK][hapmap]
rs10988530	0.86[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11515534	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11515536	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12377855	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12378396	0.93[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12379014	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12380469	0.93[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2067986	1.00[ASW][hapmap]
rs61462449	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7022881	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7028686	0.93[CEU][hapmap]
rs7032060	0.84[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7034847	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7043134	0.83[JPT][hapmap]
rs73503730	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7848837	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7851787	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7861925	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv528933	chr9:101784777-101788522	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3739799	C9orf3	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101761600-101814400	Weak transcription	Gastric	stomach
2	chr9:101761800-101785200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr9:101768800-101787200	Weak transcription	Right Atrium	heart
4	chr9:101769000-101790400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:101773000-101793600	Weak transcription	Aorta	Aorta
6	chr9:101775400-101784800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr9:101775600-101785200	Strong transcription	Adipose Nuclei	Adipose
8	chr9:101776600-101790200	Weak transcription	Fetal Intestine Small	intestine
9	chr9:101777000-101785600	Weak transcription	Thymus	Thymus
10	chr9:101777000-101788000	Weak transcription	Esophagus	oesophagus
11	chr9:101777400-101785800	Strong transcription	Fetal Stomach	stomach
12	chr9:101777800-101786000	Strong transcription	Colon Smooth Muscle	Colon
13	chr9:101779400-101785600	Weak transcription	Ovary	ovary
14	chr9:101779400-101788600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:101781200-101786000	Genic enhancers	Placenta	Placenta
16	chr9:101781200-101791800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:101781800-101784800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr9:101782000-101788400	Weak transcription	K562	blood
19	chr9:101782000-101819800	Weak transcription	Colonic Mucosa	Colon
20	chr9:101782200-101784800	Enhancers	Hela-S3	cervix
21	chr9:101782800-101784800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:101782800-101785200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:101783000-101786000	Weak transcription	Brain Anterior Caudate	brain
24	chr9:101783200-101785000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:101783200-101786000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:101783200-101786000	Weak transcription	HSMM	muscle
27	chr9:101783400-101786000	Weak transcription	Osteobl	bone
28	chr9:101783800-101785000	Strong transcription	Pancreas	Pancrea
29	chr9:101784000-101785600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:101784000-101786000	Weak transcription	NHDF-Ad	bronchial
31	chr9:101784200-101785000	Strong transcription	Right Ventricle	heart
32	chr9:101784200-101785400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:101784200-101785400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
34	chr9:101784200-101785600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:101784400-101785200	Strong transcription	Left Ventricle	heart
36	chr9:101784400-101786400	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr9:101784600-101785000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr9:101784600-101785600	Strong transcription	Rectal Smooth Muscle	rectum
39	chr9:101784600-101785800	Weak transcription	HSMMtube	muscle
40	chr9:101784600-101786600	Genic enhancers	Fetal Muscle Leg	muscle

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