Variant report

Variant	rs10512251
Chromosome Location	chr9:97763421-97763422
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:97763417-97763493	ProgFib	skin:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:97763410-97763460	NB4	blood:	n/a
2	chr9:97763410-97763460	HCF	heart:	n/a
3	chr9:97763410-97763460	SK-N-SH_RA	brain:	n/a
4	chr9:97763410-97763460	K562	blood:	n/a
5	chr9:97763410-97763460	NHBE	bronchial:	n/a
6	chr9:97763410-97763460	H1-hESC	embryonic stem cell:	embryo
7	chr9:97763410-97763460	SKMC	muscle:	n/a
8	chr9:97763410-97763460	HAEpiC	amniotic membrane:	n/a
9	chr9:97763410-97763460	MCF-7	breast:	n/a
10	chr9:97763410-97763460	HL-60	blood:	n/a
11	chr9:97763410-97763460	HNPCEpiC	eye:	n/a
12	chr9:97763410-97763460	GM12878	blood:	n/a
13	chr9:97763410-97763460	NT2-D1	testis:	n/a
14	chr9:97763410-97763460	HCT-116	colon:	n/a
15	chr9:97763410-97763460	HRCEpiC	kidney:	n/a
16	chr9:97763410-97763460	HEK293	kidney:	embryo
17	chr9:97763410-97763460	AG09309	skin:	n/a
18	chr9:97763410-97763460	AG04450	lung:	fetal
19	chr9:97763410-97763460	BJ	skin:	n/a
20	chr9:97763410-97763460	Hela-S3	cervix:	n/a
21	chr9:97763410-97763460	PFSK-1	brain:	n/a
22	chr9:97763410-97763460	GM12892	blood:	n/a
23	chr9:97763410-97763460	NH-A	brain:	n/a
24	chr9:97763410-97763460	SK-N-SH	brain:	n/a
25	chr9:97763410-97763460	Caco-2	colon:	n/a
26	chr9:97763410-97763460	GM12891	blood:	n/a
27	chr9:97763410-97763460	HRPEpiC	eye:	n/a
28	chr9:97763410-97763460	U87	brain:	n/a
29	chr9:97763410-97763460	PANC-1	pancreas:	n/a
30	chr9:97763410-97763460	ECC-1	luminal epithelium:	n/a
31	chr9:97763410-97763460	HIPEpiC	eye:	n/a
32	chr9:97763410-97763460	AG04449	skin:	fetal
33	chr9:97763410-97763460	HRE	kidney:	n/a
34	chr9:97763410-97763460	Jurkat	blood:	n/a
35	chr9:97763410-97763460	HUVEC	blood vessel:	n/a
36	chr9:97763410-97763460	SK-N-MC	brain:	n/a
37	chr9:97763410-97763460	AoSMC	blood vessel:	n/a
38	chr9:97763410-97763460	PrEC	prostate:	n/a
39	chr9:97763410-97763460	HepG2	liver:	n/a
40	chr9:97763410-97763460	HCPEpiC	choroid plexus:	n/a
41	chr9:97763410-97763460	CMK	blood:	n/a
42	chr9:97763410-97763460	NHDF-neo	bronchial:	n/a
43	chr9:97763410-97763460	T-47D	breast:	n/a
44	chr9:97763410-97763460	ProgFib	skin:	n/a
45	chr9:97763410-97763460	BE2_C	brain:	n/a
46	chr9:97763410-97763460	MCF10A-Er-Src	breast:	n/a
47	chr9:97763410-97763460	LNCaP	prostate:	n/a
48	chr9:97763410-97763460	SAEC	small airway:	n/a
49	chr9:97763410-97763460	ovcar-3	ovarian:	n/a
50	chr9:97763410-97763460	HCM	heart:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
2	chr9:97692878..97695081-chr9:97763307..97765405,2	MCF-7	breast:
3	chr9:97544710..97547210-chr9:97761164..97763494,2	MCF-7	breast:
4	chr9:97742880..97744753-chr9:97762967..97764495,2	MCF-7	breast:
5	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:

No data

Variant related genes	Relation type
C9orf3	TF binding region
C9orf3	CpG island
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1004813	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs12684072	1.00[AMR][1000 genomes]
rs12684777	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12685442	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12686500	0.85[AFR][1000 genomes]
rs1543848	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16911830	1.00[MEX][hapmap]
rs16911870	0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16911899	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16912021	1.00[MEX][hapmap]
rs28374530	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55795857	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55932459	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7024881	0.82[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7043275	1.00[AMR][1000 genomes]
rs7046628	1.00[AMR][1000 genomes]
rs72750306	1.00[AMR][1000 genomes]
rs72750343	1.00[AMR][1000 genomes]
rs72750345	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72750349	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72750353	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72750354	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72750355	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72750360	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72750361	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72750363	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72750368	0.85[AFR][1000 genomes]
rs72750381	0.85[AFR][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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97736600-97766200	Weak transcription	Right Ventricle	heart
3	chr9:97755200-97766400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:97756200-97765000	Weak transcription	Fetal Intestine Large	intestine
5	chr9:97756200-97765000	Weak transcription	Fetal Intestine Small	intestine
6	chr9:97758400-97764200	Weak transcription	Small Intestine	intestine
7	chr9:97758400-97765000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:97758400-97766000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:97758400-97766400	Weak transcription	Gastric	stomach
10	chr9:97758600-97765000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:97758600-97766400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:97758800-97764600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:97759000-97765000	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:97759000-97765000	Weak transcription	Left Ventricle	heart
15	chr9:97759000-97765200	Weak transcription	Brain Anterior Caudate	brain
16	chr9:97759200-97765000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:97759200-97765000	Weak transcription	Fetal Kidney	kidney
18	chr9:97759200-97766200	Weak transcription	Brain Angular Gyrus	brain
19	chr9:97759200-97766200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:97759400-97763600	Weak transcription	HepG2	liver
21	chr9:97759400-97764600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:97759400-97765000	Weak transcription	Pancreas	Pancrea
23	chr9:97759400-97765200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr9:97759400-97765200	Weak transcription	Brain Substantia Nigra	brain
25	chr9:97759400-97766000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr9:97759400-97766000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr9:97759400-97766200	Weak transcription	Stomach Mucosa	stomach
28	chr9:97759600-97764800	Enhancers	A549	lung
29	chr9:97759600-97765000	Weak transcription	Fetal Heart	heart
30	chr9:97759800-97765000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:97762200-97766200	Weak transcription	Placenta	Placenta
32	chr9:97762400-97764600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:97762400-97765000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:97762400-97765000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr9:97762600-97765000	Weak transcription	Colon Smooth Muscle	Colon
36	chr9:97763000-97763600	Active TSS	Right Atrium	heart
37	chr9:97763000-97763600	Enhancers	HSMMtube	muscle
38	chr9:97763000-97766000	Enhancers	Fetal Stomach	stomach
39	chr9:97763200-97763600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr9:97763200-97763600	Active TSS	Adipose Nuclei	Adipose
41	chr9:97763200-97763600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr9:97763200-97763600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr9:97763200-97763600	Enhancers	HMEC	breast
44	chr9:97763200-97763600	Flanking Active TSS	HUVEC	blood vessel
45	chr9:97763200-97763600	Flanking Active TSS	NHDF-Ad	bronchial
46	chr9:97763200-97763600	Active TSS	Osteobl	bone
47	chr9:97763200-97763800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr9:97763200-97764200	Enhancers	Fetal Lung	lung
49	chr9:97763400-97763600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:97763400-97763600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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