Variant report

Variant	rs7047684
Chromosome Location	chr9:96792790-96792791
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	chr9:96792682-96793391	HUVEC	blood vessel:	n/a	n/a
2	TBP	chr9:96792358-96793629	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr9:96792595-96793396	ECC-1	luminal epithelium:	n/a	n/a
4	USF1	chr9:96792775-96793415	A549	lung:	n/a	chr9:96793043-96793052 chr9:96793044-96793053 chr9:96793042-96793055 chr9:96793202-96793218 chr9:96793042-96793053 chr9:96793044-96793053
5	POLR2A	chr9:96792510-96793463	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr9:96792662-96793479	K562	blood:	n/a	n/a
7	POLR2A	chr9:96792555-96793449	GM19193	blood:	n/a	n/a
8	CBX3	chr9:96792211-96793222	K562	blood:	n/a	n/a
9	CEBPD	chr9:96792746-96793342	HepG2	liver:	n/a	n/a
10	ATF3	chr9:96792783-96793096	H1-hESC	embryonic stem cell:	n/a	chr9:96792968-96792977
11	USF1	chr9:96792560-96793318	A549	lung:	n/a	chr9:96793043-96793052 chr9:96793044-96793053 chr9:96793042-96793055 chr9:96793202-96793218 chr9:96793042-96793053 chr9:96793044-96793053
12	POLR2A	chr9:96792562-96793500	GM12892	blood:	n/a	n/a
13	POLR2A	chr9:96792545-96793526	HUVEC	blood vessel:	n/a	n/a
14	SETDB1	chr9:96791934-96793709	U2OS	brain:	n/a	n/a
15	MAX	chr9:96792305-96793628	ECC-1	luminal epithelium:	n/a	n/a
16	USF1	chr9:96792664-96793271	A549	lung:	n/a	chr9:96793043-96793052 chr9:96793044-96793053 chr9:96793042-96793055 chr9:96793202-96793218 chr9:96793042-96793053 chr9:96793044-96793053
17	REST	chr9:96792727-96793061	A549	lung:	n/a	chr9:96792762-96792780 chr9:96792761-96792781 chr9:96792761-96792781 chr9:96792761-96792781
18	POLR2A	chr9:96792689-96793350	HepG2	liver:	n/a	n/a
19	POLR2A	chr9:96792586-96793528	HUVEC	blood vessel:	n/a	n/a
20	CREB1	chr9:96792484-96793588	HepG2	liver:	n/a	n/a
21	TCF12	chr9:96792584-96793435	ECC-1	luminal epithelium:	n/a	chr9:96793212-96793222
22	POLR2A	chr9:96792781-96793056	GM12891	blood:	n/a	n/a
23	POLR2A	chr9:96792658-96793376	HUVEC	blood vessel:	n/a	n/a
24	USF1	chr9:96792790-96793251	H1-hESC	embryonic stem cell:	n/a	chr9:96793043-96793052 chr9:96793044-96793053 chr9:96793042-96793055 chr9:96793202-96793218 chr9:96793042-96793053 chr9:96793044-96793053
25	POLR2A	chr9:96792631-96793469	A549	lung:	n/a	n/a
26	BHLHE40	chr9:96792676-96794040	HepG2	liver:	n/a	chr9:96793043-96793052 chr9:96793044-96793053 chr9:96793042-96793055 chr9:96793202-96793218 chr9:96793044-96793053
27	TEAD4	chr9:96792785-96793077	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF1	chr9:96792508-96793516	H1-hESC	embryonic stem cell:	n/a	n/a
29	E2F6	chr9:96792507-96793330	A549	lung:	n/a	n/a
30	PML	chr9:96792606-96793395	MCF-7	breast:	n/a	n/a
31	YY1	chr9:96792560-96793327	A549	lung:	n/a	n/a
32	NFYB	chr9:96792608-96793408	K562	blood:	n/a	chr9:96793026-96793041
33	POLR2A	chr9:96792539-96793481	A549	lung:	n/a	n/a
34	IRF1	chr9:96792777-96793147	K562	blood:	n/a	n/a
35	USF1	chr9:96792629-96793279	SK-N-SH	brain:	n/a	chr9:96793043-96793052 chr9:96793044-96793053 chr9:96793042-96793055 chr9:96793202-96793218 chr9:96793042-96793053 chr9:96793044-96793053
36	MAX	chr9:96792488-96793568	H1-hESC	embryonic stem cell:	n/a	n/a
37	CREB1	chr9:96792585-96793588	HepG2	liver:	n/a	n/a
38	GATA3	chr9:96792526-96793569	A549	lung:	n/a	chr9:96792565-96792573
39	HA-E2F1	chr9:96792629-96793730	MCF-7	breast:	n/a	chr9:96793400-96793407 chr9:96793400-96793407 chr9:96793400-96793407
40	POLR2A	chr9:96791349-96793598	HepG2	liver:	n/a	n/a
41	CREB1	chr9:96792747-96793580	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr9:96792670-96793236	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr9:96792721-96793370	GM12891	blood:	n/a	n/a
44	USF2	chr9:96792339-96794033	Hela-S3	cervix:	n/a	chr9:96793043-96793052 chr9:96793044-96793053 chr9:96793042-96793055 chr9:96793202-96793218 chr9:96793044-96793053
45	USF1	chr9:96792761-96793501	K562	blood:	n/a	chr9:96793043-96793052 chr9:96793044-96793053 chr9:96793042-96793055 chr9:96793202-96793218 chr9:96793042-96793053 chr9:96793044-96793053
46	USF1	chr9:96792762-96793378	A549	lung:	n/a	chr9:96793043-96793052 chr9:96793044-96793053 chr9:96793042-96793055 chr9:96793202-96793218 chr9:96793042-96793053 chr9:96793044-96793053
47	ETS1	chr9:96792621-96793347	K562	blood:	n/a	chr9:96792964-96792975 chr9:96792726-96792737 chr9:96792726-96792743 chr9:96792723-96792738
48	USF1	chr9:96792740-96793569	K562	blood:	n/a	chr9:96793043-96793052 chr9:96793044-96793053 chr9:96793042-96793055 chr9:96793202-96793218 chr9:96793042-96793053 chr9:96793044-96793053
49	POLR2A	chr9:96792546-96793392	SK-N-MC	brain:	n/a	n/a
50	TAF1	chr9:96792700-96793081	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:40834828..40835357-chr9:96792773..96793579,2	Hela-S3	cervix:
2	chr9:96791676..96794493-chr9:96936767..96941836,4	MCF-7	breast:
3	chr9:96791956..96794354-chr9:96926207..96931491,6	MCF-7	breast:
4	chr9:96792323..96794528-chr9:96927672..96930924,4	MCF-7	breast:
5	chr9:96792104..96794426-chr9:96846620..96848608,2	MCF-7	breast:
6	chr9:96790378..96795979-chr9:96796527..96801819,13	MCF-7	breast:
7	chr9:96790823..96795467-chr9:96925835..96932235,7	K562	blood:
8	chr12:54673338..54674504-chr9:96792757..96793584,3	Hela-S3	cervix:
9	chr9:96791026..96792800-chr9:96856915..96858416,2	MCF-7	breast:
10	chr9:96790406..96793524-chr9:96937356..96939962,3	MCF-7	breast:
11	chr19:1248296..1248925-chr9:96792564..96793476,2	Hela-S3	cervix:
12	chr9:96791020..96793870-chr9:96797908..96800825,2	K562	blood:
13	chr9:96790341..96794271-chr9:96926817..96931236,5	K562	blood:
14	chr9:96791853..96794356-chr9:96860367..96862558,2	MCF-7	breast:

Variant related genes	Relation type
PTPDC1	TF binding region
ENSG00000145592	Chromatin interaction
ENSG00000094916	Chromatin interaction
ENSG00000167470	Chromatin interaction
ENSG00000269946	Chromatin interaction
ENSG00000227666	Chromatin interaction
ENSG00000199133	Chromatin interaction
ENSG00000158079	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000269929	Chromatin interaction
ENSG00000199165	Chromatin interaction
ENSG00000199072	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10993017	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs10993047	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs11788176	0.91[CEU][hapmap]
rs11789837	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11791859	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793856	0.82[CEU][hapmap]
rs11999153	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12004383	0.86[CEU][hapmap]
rs12684081	0.84[CEU][hapmap]
rs1411861	0.92[CEU][hapmap]
rs1539282	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2039313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34169833	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4319160	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4514041	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7855830	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7870790	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7872984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv3426132	chr9:96782446-96794518	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7047684	C9orf3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96791800-96793600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr9:96791800-96793800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr9:96791800-96794000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr9:96791800-96794200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:96792000-96792800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr9:96792000-96792800	Flanking Active TSS	HMEC	breast
7	chr9:96792000-96793600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr9:96792000-96793600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr9:96792000-96793600	Active TSS	Duodenum Mucosa	Duodenum
10	chr9:96792000-96793600	Active TSS	Fetal Kidney	kidney
11	chr9:96792000-96793800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr9:96792000-96793800	Active TSS	Placenta Amnion	Placenta Amnion
13	chr9:96792000-96794200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:96792200-96792800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr9:96792200-96792800	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr9:96792200-96792800	Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr9:96792200-96792800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr9:96792200-96792800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr9:96792200-96792800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr9:96792200-96792800	Active TSS	Brain Germinal Matrix	brain
21	chr9:96792200-96792800	Flanking Active TSS	Fetal Thymus	thymus
22	chr9:96792200-96792800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr9:96792200-96792800	Flanking Active TSS	HUVEC	blood vessel
24	chr9:96792200-96792800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr9:96792200-96793200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:96792200-96793600	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr9:96792200-96793600	Active TSS	Brain Substantia Nigra	brain
28	chr9:96792200-96793600	Active TSS	Fetal Brain Male	brain
29	chr9:96792200-96793800	Active TSS	H9 Cell Line	embryonic stem cell
30	chr9:96792200-96793800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr9:96792200-96793800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:96792200-96793800	Active TSS	Muscle Satellite Cultured Cells	--
33	chr9:96792200-96793800	Active TSS	Brain Anterior Caudate	brain
34	chr9:96792200-96793800	Active TSS	Brain Hippocampus Middle	brain
35	chr9:96792200-96793800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr9:96792200-96793800	Active TSS	Rectal Smooth Muscle	rectum
37	chr9:96792200-96793800	Active TSS	A549	lung
38	chr9:96792200-96794000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:96792200-96794000	Active TSS	Colonic Mucosa	Colon
40	chr9:96792200-96794000	Active TSS	Fetal Intestine Small	intestine
41	chr9:96792200-96794000	Active TSS	HSMM	muscle
42	chr9:96792200-96794200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:96792200-96794200	Active TSS	Fetal Brain Female	brain
44	chr9:96792200-96794200	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr9:96792200-96794400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr9:96792200-96794400	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr9:96792200-96794400	Active TSS	Right Ventricle	heart
48	chr9:96792200-96794600	Active TSS	HSMMtube	muscle
49	chr9:96792400-96792800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:96792400-96792800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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