Variant report

Variant	rs1215114
Chromosome Location	chr9:15307463-15307464
allele	C/G
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	MAX	chr9:15307123-15307754	HepG2	liver:	n/a	n/a
2	MXI1	chr9:15306053-15307720	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:15306981-15307669	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:15306801-15307580	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr9:15307399-15307583	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr9:15307380-15307530	GM12864	blood:	n/a	n/a
7	IRF1	chr9:15307115-15307603	K562	blood:	n/a	n/a
8	SP4	chr9:15306787-15307580	H1-hESC	embryonic stem cell:	n/a	chr9:15306977-15306993 chr9:15307282-15307293 chr9:15306979-15306995
9	YY1	chr9:15307126-15307559	SK-N-SH_RA	brain:	n/a	n/a
10	CTCF	chr9:15307320-15307470	HPF	lung:	n/a	chr9:15307365-15307378 chr9:15307362-15307375 chr9:15307368-15307381
11	PAX5	chr9:15307437-15307801	GM12892	blood:	n/a	n/a
12	MAX	chr9:15307180-15307661	NB4	blood:	n/a	n/a
13	CHD2	chr9:15307417-15307617	K562	blood:	n/a	n/a
14	CTCF	chr9:15307372-15307488	H1-hESC	embryonic stem cell:	n/a	n/a
15	JUND	chr9:15307171-15307857	K562	blood:	n/a	n/a
16	POLR2A	chr9:15306716-15307478	IMR90	lung:	n/a	n/a
17	SIN3AK20	chr9:15306818-15307900	MCF-7	breast:	n/a	n/a
18	CTCF	chr9:15307379-15307703	GM19239	blood:	n/a	chr9:15307550-15307559
19	MAZ	chr9:15305818-15308209	IMR90	lung:	n/a	chr9:15306783-15306793
20	HMGN3	chr9:15306828-15307744	K562	blood:	n/a	n/a
21	CTCF	chr9:15307421-15307692	GM12891	blood:	n/a	chr9:15307550-15307559
22	CTCF	chr9:15307420-15307570	HCPEpiC	choroid plexus:	n/a	chr9:15307550-15307559
23	MAZ	chr9:15307089-15307514	GM12878	blood:	n/a	n/a
24	POLR2A	chr9:15306001-15307712	HepG2	liver:	n/a	n/a
25	MAX	chr9:15307059-15307773	MCF-7	breast:	n/a	n/a
26	NR2F2	chr9:15307040-15307878	MCF-7	breast:	n/a	n/a
27	CTCF	chr9:15307383-15307676	MCF-7	breast:	n/a	chr9:15307550-15307559
28	STAT3	chr9:15307212-15307606	MCF10A-Er-Src	breast:	n/a	n/a
29	CTCF	chr9:15307380-15307530	HRPEpiC	eye:	n/a	n/a
30	TBP	chr9:15307088-15307527	HepG2	liver:	n/a	n/a
31	ZNF143	chr9:15307148-15307546	GM12878	blood:	n/a	n/a
32	ZEB1	chr9:15307305-15307709	GM12878	blood:	n/a	chr9:15307489-15307498 chr9:15307547-15307556
33	CTCF	chr9:15307420-15307570	A549	lung:	n/a	chr9:15307550-15307559
34	CTCF	chr9:15307302-15307631	H1-hESC	embryonic stem cell:	n/a	chr9:15307365-15307378 chr9:15307550-15307559 chr9:15307362-15307375 chr9:15307368-15307381
35	CTCF	chr9:15307406-15307686	GM19240	blood:	n/a	chr9:15307550-15307559
36	CTCF	chr9:15307400-15307550	HPF	lung:	n/a	n/a
37	STAT3	chr9:15307221-15307804	MCF10A-Er-Src	breast:	n/a	n/a
38	CTCF	chr9:15307380-15307530	GM12866	blood:	n/a	n/a
39	RCOR1	chr9:15307051-15307662	K562	blood:	n/a	n/a
40	STAT1	chr9:15307150-15307577	GM12878	blood:	n/a	n/a
41	ELF1	chr9:15307077-15307536	K562	blood:	n/a	n/a
42	MYC	chr9:15306979-15307601	H1-hESC	embryonic stem cell:	n/a	n/a
43	TAF1	chr9:15306829-15307693	ECC-1	luminal epithelium:	n/a	n/a
44	YY1	chr9:15306666-15307687	HepG2	liver:	n/a	chr9:15306982-15306991
45	ELF1	chr9:15307135-15307523	HepG2	liver:	n/a	n/a
46	POLR2A	chr9:15306860-15307566	HUVEC	blood vessel:	n/a	n/a
47	E2F6	chr9:15307245-15307752	H1-hESC	embryonic stem cell:	n/a	chr9:15307372-15307382
48	POLR2A	chr9:15306968-15307639	HepG2	liver:	n/a	n/a
49	STAT3	chr9:15307213-15307614	MCF10A-Er-Src	breast:	n/a	n/a
50	MAX	chr9:15307156-15307610	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15306135..15309581-chr9:15420818..15425516,6	MCF-7	breast:

Variant related genes	Relation type
TTC39B	TF binding region
ENSG00000164975	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10435728	0.80[ASN][1000 genomes]
rs10738391	0.80[ASN][1000 genomes]
rs10810372	0.80[JPT][hapmap]
rs10961962	0.80[JPT][hapmap]
rs491322	0.85[CEU][hapmap]
rs570474	0.84[CHB][hapmap];0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs571888	0.84[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs6474902	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761505	chr9:15274373-15319613	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv613650	chr9:15296119-15378449	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv613651	chr9:15296355-15358157	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1015960	chr9:15296783-15380657	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv524849	chr9:15299590-15362057	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1215114	TTC39B	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15304200-15307600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:15305400-15307600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr9:15305600-15307600	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr9:15305600-15307600	Active TSS	Rectal Smooth Muscle	rectum
5	chr9:15305600-15307800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:15305600-15307800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:15305600-15307800	Active TSS	Aorta	Aorta
8	chr9:15305600-15308000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:15305800-15307600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr9:15305800-15307600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr9:15305800-15307600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr9:15305800-15307600	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr9:15305800-15307600	Active TSS	Esophagus	oesophagus
14	chr9:15305800-15307600	Active TSS	Psoas Muscle	Psoas
15	chr9:15305800-15307600	Active TSS	NHDF-Ad	bronchial
16	chr9:15305800-15307800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr9:15305800-15307800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr9:15305800-15307800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr9:15305800-15307800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr9:15305800-15307800	Active TSS	Right Atrium	heart
21	chr9:15305800-15307800	Active TSS	HSMMtube	muscle
22	chr9:15306000-15307600	Active TSS	H1 Cell Line	embryonic stem cell
23	chr9:15306000-15307600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr9:15306000-15307600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr9:15306000-15307600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:15306000-15307600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:15306000-15307600	Active TSS	Brain Anterior Caudate	brain
28	chr9:15306000-15307600	Active TSS	Lung	lung
29	chr9:15306000-15307600	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr9:15306000-15307600	Active TSS	HSMM	muscle
31	chr9:15306000-15307800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr9:15306000-15307800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr9:15306000-15307800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr9:15306000-15307800	Active TSS	Fetal Kidney	kidney
35	chr9:15306000-15307800	Active TSS	Fetal Lung	lung
36	chr9:15306000-15307800	Active TSS	Ovary	ovary
37	chr9:15306000-15307800	Active TSS	Right Ventricle	heart
38	chr9:15306000-15307800	Active TSS	A549	lung
39	chr9:15306000-15308000	Active TSS	Brain Cingulate Gyrus	brain
40	chr9:15306200-15307600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:15306200-15307600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:15306200-15307600	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr9:15306200-15307600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:15306200-15307600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:15306200-15307600	Active TSS	Small Intestine	intestine
46	chr9:15306200-15307800	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr9:15306200-15307800	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr9:15306200-15307800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:15306200-15307800	Active TSS	Colon Smooth Muscle	Colon
50	chr9:15306200-15308000	Active TSS	Brain Substantia Nigra	brain

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