Variant report

Variant	rs10491742
Chromosome Location	chr9:12775488-12775489
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	GTF2F1	chr9:12774743-12777007	Hela-S3	cervix:	n/a	n/a
2	TCF7L2	chr9:12774846-12776815	HCT-116	colon:	n/a	n/a
3	SIN3A	chr9:12774804-12776765	H1-hESC	embryonic stem cell:	n/a	chr9:12776384-12776395 chr9:12776121-12776132
4	SIN3AK20	chr9:12774759-12777675	MCF-7	breast:	n/a	n/a
5	KAP1	chr9:12774695-12776971	HEK293	kidney:	n/a	n/a
6	POLR2A	chr9:12775437-12776712	MCF-7	breast:	n/a	n/a
7	POLR2A	chr9:12774834-12779295	MCF10A-Er-Src	breast:	n/a	n/a
8	MAX	chr9:12775316-12776850	HepG2	liver:	n/a	n/a
9	SIN3AK20	chr9:12774725-12775489	MCF-7	breast:	n/a	n/a
10	CHD2	chr9:12774814-12776850	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr9:12774693-12778064	IMR90	lung:	n/a	chr9:12777846-12777861
12	MXI1	chr9:12774877-12776754	HepG2	liver:	n/a	n/a
13	POLR2A	chr9:12775449-12776630	A549	lung:	n/a	n/a
14	REST	chr9:12774805-12775588	A549	lung:	n/a	n/a
15	TCF12	chr9:12774654-12777141	A549	lung:	n/a	chr9:12776538-12776548
16	SMC3	chr9:12774741-12777261	SK-N-SH	brain:	n/a	chr9:12776171-12776181
17	CTCF	chr9:12775480-12775630	BE2_C	brain:	n/a	n/a
18	BCL3	chr9:12774751-12775592	A549	lung:	n/a	chr9:12775208-12775217
19	RFX5	chr9:12774750-12775563	Hela-S3	cervix:	n/a	n/a
20	USF2	chr9:12774780-12776047	Hela-S3	cervix:	n/a	chr9:12775512-12775528
21	CREB1	chr9:12775422-12776718	A549	lung:	n/a	n/a
22	CTCF	chr9:12775440-12775590	HBMEC	blood vessel:	n/a	n/a
23	CTCF	chr9:12775460-12775610	HMF	breast:	n/a	n/a
24	ZBTB7A	chr9:12775465-12775684	HepG2	liver:	n/a	n/a
25	ZBTB7A	chr9:12775437-12775904	ECC-1	luminal epithelium:	n/a	n/a
26	GATA2	chr9:12774900-12777412	SH-SY5Y	brain:	n/a	chr9:12777001-12777011 chr9:12777001-12777010 chr9:12776805-12776815 chr9:12777003-12777013 chr9:12777003-12777010
27	MAX	chr9:12774649-12777128	A549	lung:	n/a	n/a
28	HEY1	chr9:12774793-12777037	HepG2	liver:	n/a	n/a
29	POLR2A	chr9:12774806-12777502	HepG2	liver:	n/a	n/a
30	CTCF	chr9:12775470-12775586	MCF-7	breast:	n/a	n/a
31	POLR2A	chr9:12775354-12777021	HCT-116	colon:	n/a	n/a
32	POLR2A	chr9:12774751-12777159	HCT-116	colon:	n/a	n/a
33	POLR2A	chr9:12774828-12779200	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr9:12775442-12776693	MCF-7	breast:	n/a	n/a
35	GATA3	chr9:12775349-12776819	MCF-7	breast:	n/a	chr9:12776805-12776815
36	HEY1	chr9:12775434-12775790	HepG2	liver:	n/a	n/a
37	POLR2A	chr9:12774850-12775688	U87	brain:	n/a	n/a
38	CTCF	chr9:12775400-12775550	AG09319	gingival:	n/a	n/a
39	YY1	chr9:12774682-12775557	SK-N-SH_RA	brain:	n/a	n/a
40	POLR2A	chr9:12775453-12776668	A549	lung:	n/a	n/a
41	POLR2A	chr9:12775407-12776802	A549	lung:	n/a	n/a
42	POLR2A	chr9:12775439-12776805	HepG2	liver:	n/a	n/a
43	RCOR1	chr9:12774787-12777085	Hela-S3	cervix:	n/a	n/a
44	BHLHE40	chr9:12775478-12776767	HepG2	liver:	n/a	chr9:12775512-12775528 chr9:12776042-12776058
45	MAX	chr9:12774771-12776961	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr9:12775339-12776734	A549	lung:	n/a	n/a
47	CTCF	chr9:12775400-12775550	HBMEC	blood vessel:	n/a	n/a
48	CEBPB	chr9:12774779-12777732	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr9:12774819-12778894	IMR90	lung:	n/a	n/a
50	CTCF	chr9:12775481-12775622	Fibrobl	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:32895532..32897847-chr9:12774427..12776236,2	MCF-7	breast:
2	chr9:12774954..12777056-chr9:12883374..12886318,3	MCF-7	breast:
3	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
4	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:

Variant related genes	Relation type
LURAP1L	TF binding region
ENSG00000269093	Chromatin interaction
ENSG00000178904	Chromatin interaction
ENSG00000267213	Chromatin interaction
ENSG00000222658	Chromatin interaction
ENSG00000235448	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1063380	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1074789	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs10756405	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10756406	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs10809826	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10809836	0.83[EUR][1000 genomes]
rs10960762	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs10960774	0.81[AMR][1000 genomes]
rs10960775	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10960779	0.84[EUR][1000 genomes]
rs10960781	0.83[EUR][1000 genomes]
rs12115198	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12379260	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap]
rs12552462	0.81[EUR][1000 genomes]
rs1326788	0.84[EUR][1000 genomes]
rs1326789	0.84[EUR][1000 genomes]
rs1326790	0.84[EUR][1000 genomes]
rs1326791	0.84[EUR][1000 genomes]
rs1326792	0.84[EUR][1000 genomes]
rs1326798	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs13284453	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs13284898	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs13289304	0.81[EUR][1000 genomes]
rs13302551	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1543587	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs17346161	1.00[CHB][hapmap]
rs2209271	0.80[EUR][1000 genomes]
rs2209277	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2224863	1.00[CHB][hapmap]
rs2733830	1.00[CHB][hapmap]
rs2733831	1.00[CHB][hapmap]
rs2733832	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap]
rs2733833	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2733834	1.00[CHB][hapmap]
rs2733836	1.00[CHB][hapmap]
rs2762457	1.00[ASN][1000 genomes]
rs2762458	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs2762461	1.00[CHB][hapmap]
rs2762463	1.00[CHB][hapmap]
rs2762464	1.00[CHB][hapmap]
rs4741245	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs683	1.00[CHB][hapmap]
rs7021368	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7023927	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7025678	0.83[EUR][1000 genomes]
rs7025771	0.83[EUR][1000 genomes]
rs7025842	0.83[EUR][1000 genomes]
rs7025914	0.83[EUR][1000 genomes]
rs7025953	0.83[EUR][1000 genomes]
rs7030485	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7035500	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7036011	0.84[EUR][1000 genomes]
rs7039325	0.84[EUR][1000 genomes]
rs7466623	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs910	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs927868	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs927869	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs958073	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10491742	C9orf150	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12774200-12776600	Active TSS	Fetal Lung	lung
2	chr9:12774600-12776600	Active TSS	Brain Cingulate Gyrus	brain
3	chr9:12774600-12776600	Active TSS	Fetal Kidney	kidney
4	chr9:12774600-12776600	Active TSS	NH-A	brain
5	chr9:12774600-12776800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:12774600-12778000	Active TSS	NHDF-Ad	bronchial
7	chr9:12774800-12775600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
8	chr9:12774800-12775800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:12774800-12776000	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr9:12774800-12776000	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr9:12774800-12776200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr9:12774800-12776200	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr9:12774800-12776200	Active TSS	Fetal Brain Male	brain
14	chr9:12774800-12776200	Bivalent/Poised TSS	GM12878-XiMat	blood
15	chr9:12774800-12776400	Active TSS	Brain Germinal Matrix	brain
16	chr9:12774800-12776400	Active TSS	Fetal Brain Female	brain
17	chr9:12774800-12776600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:12774800-12776600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr9:12774800-12776600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr9:12774800-12776600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr9:12774800-12776600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
22	chr9:12774800-12776600	Active TSS	Muscle Satellite Cultured Cells	--
23	chr9:12774800-12776600	Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr9:12774800-12776600	Active TSS	Adipose Nuclei	Adipose
25	chr9:12774800-12776600	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr9:12774800-12776600	Active TSS	Duodenum Mucosa	Duodenum
27	chr9:12774800-12776600	Active TSS	Fetal Muscle Leg	muscle
28	chr9:12774800-12776600	Active TSS	Hela-S3	cervix
29	chr9:12774800-12776600	Active TSS	HSMMtube	muscle
30	chr9:12774800-12776800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:12774800-12776800	Bivalent/Poised TSS	HepG2	liver
32	chr9:12774800-12777000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:12774800-12777000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:12774800-12777000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr9:12774800-12777000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:12774800-12777000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:12774800-12777000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:12774800-12777000	Active TSS	Brain Substantia Nigra	brain
39	chr9:12774800-12777000	Active TSS	Left Ventricle	heart
40	chr9:12774800-12777000	Active TSS	Right Ventricle	heart
41	chr9:12774800-12777000	Active TSS	Stomach Mucosa	stomach
42	chr9:12774800-12777200	Active TSS	Psoas Muscle	Psoas
43	chr9:12774800-12777200	Active TSS	Osteobl	bone
44	chr9:12774800-12777400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:12774800-12777400	Active TSS	Brain Angular Gyrus	brain
46	chr9:12774800-12777400	Active TSS	Brain Anterior Caudate	brain
47	chr9:12774800-12777400	Active TSS	Brain Hippocampus Middle	brain
48	chr9:12774800-12777400	Active TSS	Fetal Muscle Trunk	muscle
49	chr9:12774800-12777400	Active TSS	Ovary	ovary
50	chr9:12774800-12777400	Active TSS	A549	lung

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