Variant report

Variant	rs11078409
Chromosome Location	chr17:17876296-17876297
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	MXI1	chr17:17875948-17876390	K562	blood:	n/a	chr17:17876149-17876158
2	SIN3AK20	chr17:17875989-17876419	HepG2	liver:	n/a	n/a
3	MXI1	chr17:17873901-17876944	IMR90	lung:	n/a	chr17:17876149-17876158
4	MYBL2	chr17:17875881-17876403	HepG2	liver:	n/a	n/a
5	NFYA	chr17:17875417-17876342	Hela-S3	cervix:	n/a	chr17:17876080-17876090
6	GABPA	chr17:17875523-17876540	A549	lung:	n/a	chr17:17875762-17875771
7	SMC3	chr17:17874813-17876389	Hela-S3	cervix:	n/a	chr17:17875143-17875153 chr17:17875045-17875059
8	ZNF143	chr17:17875694-17876306	K562	blood:	n/a	n/a
9	ZKSCAN1	chr17:17875680-17876366	Hela-S3	cervix:	n/a	n/a
10	MAX	chr17:17875406-17876373	A549	lung:	n/a	chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876153-17876161 chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876150-17876159
11	MYC	chr17:17875573-17876320	K562	blood:	n/a	chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876153-17876161 chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876150-17876159
12	RXRA	chr17:17875779-17876343	HepG2	liver:	n/a	chr17:17876163-17876177 chr17:17876163-17876176 chr17:17876159-17876179
13	SPI1	chr17:17875865-17876457	HL-60	blood:	n/a	chr17:17876191-17876204 chr17:17876193-17876202
14	SP1	chr17:17875464-17876387	H1-hESC	embryonic stem cell:	n/a	chr17:17875929-17875938 chr17:17875761-17875771 chr17:17875545-17875559 chr17:17875761-17875770 chr17:17875761-17875771 chr17:17875761-17875775 chr17:17876062-17876071 chr17:17875928-17875937 chr17:17875802-17875823 chr17:17875760-17875772 chr17:17875761-17875770 chr17:17875916-17875927 chr17:17875760-17875772 chr17:17875762-17875771 chr17:17875927-17875938
15	ELK1	chr17:17875679-17876308	Hela-S3	cervix:	n/a	n/a
16	SPI1	chr17:17876051-17876313	GM12878	blood:	n/a	chr17:17876191-17876204 chr17:17876193-17876202
17	STAT1	chr17:17875629-17876323	GM12878	blood:	n/a	n/a
18	CREB1	chr17:17875605-17876413	H1-hESC	embryonic stem cell:	n/a	n/a
19	FOS	chr17:17875607-17876349	K562	blood:	n/a	n/a
20	MAZ	chr17:17874987-17876373	Hela-S3	cervix:	n/a	chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876153-17876161 chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876150-17876159
21	GABPA	chr17:17875599-17876318	HepG2	liver:	n/a	chr17:17875762-17875771
22	ETS1	chr17:17876134-17876378	K562	blood:	n/a	chr17:17876298-17876311
23	CEBPB	chr17:17875931-17876300	H1-hESC	embryonic stem cell:	n/a	n/a
24	SIN3A	chr17:17875492-17876738	GM12878	blood:	n/a	chr17:17876149-17876158 chr17:17876151-17876160
25	USF2	chr17:17875741-17876375	GM12878	blood:	n/a	chr17:17876148-17876159 chr17:17876144-17876165 chr17:17876150-17876159 chr17:17876149-17876158 chr17:17876151-17876160 chr17:17876150-17876159 chr17:17876148-17876161
26	POLR2A	chr17:17875479-17876851	MCF10A-Er-Src	breast:	n/a	n/a
27	CEBPB	chr17:17875846-17876402	A549	lung:	n/a	n/a
28	NFYB	chr17:17875550-17876298	K562	blood:	n/a	chr17:17876080-17876090 chr17:17875863-17875878
29	SIN3AK20	chr17:17875497-17876465	H1-hESC	embryonic stem cell:	n/a	n/a
30	USF1	chr17:17875689-17876446	SK-N-SH	brain:	n/a	chr17:17876144-17876165 chr17:17876150-17876159 chr17:17876149-17876158 chr17:17876151-17876160 chr17:17876150-17876159 chr17:17876148-17876161
31	MAX	chr17:17875347-17876411	A549	lung:	n/a	chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876153-17876161 chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876150-17876159
32	CREB1	chr17:17875467-17876606	GM12878	blood:	n/a	n/a
33	ELF1	chr17:17875654-17876409	A549	lung:	n/a	n/a
34	CREB1	chr17:17875602-17876327	ECC-1	luminal epithelium:	n/a	n/a
35	MAX	chr17:17874832-17876521	A549	lung:	n/a	chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876153-17876161 chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876150-17876159
36	USF2	chr17:17875945-17876346	H1-hESC	embryonic stem cell:	n/a	chr17:17876148-17876159 chr17:17876144-17876165 chr17:17876150-17876159 chr17:17876149-17876158 chr17:17876151-17876160 chr17:17876150-17876159 chr17:17876148-17876161
37	NR2C2	chr17:17875709-17876354	Hela-S3	cervix:	n/a	chr17:17876162-17876177
38	CREB1	chr17:17875541-17876355	ECC-1	luminal epithelium:	n/a	n/a
39	ELF1	chr17:17875705-17876316	K562	blood:	n/a	n/a
40	CREB1	chr17:17875288-17876472	HepG2	liver:	n/a	n/a
41	MAX	chr17:17875343-17876403	SK-N-SH	brain:	n/a	chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876153-17876161 chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876150-17876159
42	SP1	chr17:17875481-17876354	GM12878	blood:	n/a	chr17:17875929-17875938 chr17:17875761-17875771 chr17:17875545-17875559 chr17:17875761-17875770 chr17:17875761-17875771 chr17:17875761-17875775 chr17:17876062-17876071 chr17:17875928-17875937 chr17:17875802-17875823 chr17:17875760-17875772 chr17:17875761-17875770 chr17:17875916-17875927 chr17:17875760-17875772 chr17:17875762-17875771 chr17:17875927-17875938
43	GTF2F1	chr17:17875883-17876338	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAX	chr17:17875536-17876384	GM12878	blood:	n/a	chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876153-17876161 chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876150-17876159
45	POLR2A	chr17:17875341-17876451	H1-neurons	neurons:	n/a	n/a
46	HCFC1	chr17:17874909-17876897	Hela-S3	cervix:	n/a	n/a
47	GTF2F1	chr17:17875862-17876318	K562	blood:	n/a	n/a
48	USF1	chr17:17875758-17876415	ECC-1	luminal epithelium:	n/a	chr17:17876144-17876165 chr17:17876150-17876159 chr17:17876149-17876158 chr17:17876151-17876160 chr17:17876150-17876159 chr17:17876148-17876161
49	GABPA	chr17:17875513-17876533	SK-N-SH	brain:	n/a	chr17:17875762-17875771
50	CEBPB	chr17:17875701-17876382	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17874682..17878997-chr17:17883276..17886236,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C17orf39-2	chr17:17876281-17876413	NONHSAT146126

Variant related genes	Relation type
TOM1L2	TF binding region
ENSG00000230273	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11078406	0.87[AFR][1000 genomes]
rs11078408	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11658257	0.87[ASN][1000 genomes]
rs11870660	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12150369	0.80[AMR][1000 genomes]
rs12603148	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12940282	0.85[ASN][1000 genomes]
rs28537385	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2955350	0.90[ASN][1000 genomes]
rs2955352	0.81[ASN][1000 genomes]
rs2955353	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2955354	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2955359	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2955369	0.89[ASN][1000 genomes]
rs2955370	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2955372	0.90[ASN][1000 genomes]
rs2955377	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2955378	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2955380	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2955381	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2955384	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2955385	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3935505	0.93[ASN][1000 genomes]
rs3935506	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4299203	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4365348	0.80[AMR][1000 genomes]
rs4368210	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4459604	0.80[AMR][1000 genomes]
rs4471742	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4506969	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4584886	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4635395	0.94[AFR][1000 genomes]
rs4924832	0.82[AMR][1000 genomes]
rs4925133	0.86[EUR][1000 genomes]
rs4925135	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs57728924	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59304093	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62072048	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62072050	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6502631	0.83[AMR][1000 genomes]
rs6502632	0.83[AMR][1000 genomes]
rs6502633	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6502634	0.87[ASN][1000 genomes]
rs7207461	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7207821	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7212167	0.82[AMR][1000 genomes]
rs7214002	0.95[AFR][1000 genomes]
rs7215524	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7219320	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7223696	0.80[AMR][1000 genomes]
rs7224047	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7503738	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8068175	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8069811	0.80[AMR][1000 genomes]
rs8070731	0.92[ASN][1000 genomes]
rs8071238	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8075189	0.84[AMR][1000 genomes]
rs8076747	0.93[AFR][1000 genomes]
rs8080602	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9896837	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9897761	0.80[AMR][1000 genomes]
rs9908832	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9911850	0.80[AMR][1000 genomes]
rs9912096	0.85[AMR][1000 genomes]
rs9914127	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11078409	LRRC48	cis	brain	BrainEAC
rs11078409	AC122129.1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17873800-17876400	Active TSS	Esophagus	oesophagus
2	chr17:17873800-17876600	Active TSS	Right Atrium	heart
3	chr17:17874200-17876600	Active TSS	Left Ventricle	heart
4	chr17:17874400-17876400	Active TSS	Gastric	stomach
5	chr17:17874400-17876600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr17:17874400-17876600	Active TSS	Aorta	Aorta
7	chr17:17874400-17876800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr17:17874600-17876400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr17:17874600-17876600	Active TSS	Fetal Kidney	kidney
10	chr17:17874600-17876600	Active TSS	HSMM	muscle
11	chr17:17874600-17876600	Active TSS	NHDF-Ad	bronchial
12	chr17:17874600-17876800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr17:17874800-17876400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr17:17874800-17876400	Active TSS	NHLF	lung
15	chr17:17874800-17876600	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr17:17874800-17876600	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr17:17874800-17876600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:17874800-17876600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr17:17874800-17876600	Active TSS	Ovary	ovary
20	chr17:17874800-17876600	Active TSS	HSMMtube	muscle
21	chr17:17874800-17876800	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr17:17874800-17877000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:17875000-17876400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr17:17875000-17876400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:17875000-17876400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr17:17875000-17876400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
27	chr17:17875000-17876400	Active TSS	Brain Anterior Caudate	brain
28	chr17:17875000-17876400	Active TSS	Rectal Smooth Muscle	rectum
29	chr17:17875000-17876400	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr17:17875000-17876400	Active TSS	Small Intestine	intestine
31	chr17:17875000-17876400	Active TSS	Stomach Mucosa	stomach
32	chr17:17875000-17876400	Active TSS	Hela-S3	cervix
33	chr17:17875000-17876400	Active TSS	HMEC	breast
34	chr17:17875000-17876400	Active TSS	NH-A	brain
35	chr17:17875000-17876400	Active TSS	NHEK	skin
36	chr17:17875000-17876400	Active TSS	Osteobl	bone
37	chr17:17875000-17876600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr17:17875000-17876600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr17:17875000-17876600	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr17:17875000-17876600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr17:17875000-17876600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr17:17875000-17876600	Active TSS	Colon Smooth Muscle	Colon
43	chr17:17875000-17876600	Active TSS	Fetal Intestine Small	intestine
44	chr17:17875000-17876600	Active TSS	Right Ventricle	heart
45	chr17:17875000-17876800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr17:17875000-17876800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr17:17875200-17876400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:17875200-17876400	Active TSS	Primary T cells from cord blood	blood
49	chr17:17875200-17876400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr17:17875200-17876400	Active TSS	Primary T killer memory cells from peripheral blood	blood

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