Variant report

Variant	rs59304093
Chromosome Location	chr17:17875407-17875408
allele	A/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	chr17:17873901-17876944	IMR90	lung:	n/a	chr17:17876149-17876158
2	SMC3	chr17:17874813-17876389	Hela-S3	cervix:	n/a	chr17:17875143-17875153 chr17:17875045-17875059
3	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
4	POLR2A	chr17:17875401-17876021	SK-N-MC	brain:	n/a	n/a
5	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
6	POLR2A	chr17:17875317-17875850	MCF-7	breast:	n/a	n/a
7	POLR2A	chr17:17875308-17875989	U87	brain:	n/a	n/a
8	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
9	YY1	chr17:17875385-17876134	SK-N-SH_RA	brain:	n/a	chr17:17875618-17875635 chr17:17875762-17875771
10	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
11	YY1	chr17:17875199-17876042	HepG2	liver:	n/a	chr17:17875618-17875635 chr17:17875762-17875771
12	POLR2A	chr17:17875291-17876026	U87	brain:	n/a	n/a
13	CREB1	chr17:17875288-17876472	HepG2	liver:	n/a	n/a
14	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
15	POLR2A	chr17:17875341-17876451	H1-neurons	neurons:	n/a	n/a
16	HCFC1	chr17:17874909-17876897	Hela-S3	cervix:	n/a	n/a
17	JUND	chr17:17875367-17876037	A549	lung:	n/a	n/a
18	EBF1	chr17:17874992-17875683	GM12878	blood:	n/a	n/a
19	MXI1	chr17:17874784-17876463	Hela-S3	cervix:	n/a	chr17:17876149-17876158
20	EBF1	chr17:17874851-17875771	GM12878	blood:	n/a	n/a
21	PBX3	chr17:17875381-17876489	A549	lung:	n/a	n/a
22	MXI1	chr17:17874358-17876911	SK-N-SH	brain:	n/a	chr17:17876149-17876158
23	CREB1	chr17:17875226-17876465	A549	lung:	n/a	n/a
24	SIN3AK20	chr17:17875203-17876541	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr17:17875389-17875940	HUVEC	blood vessel:	n/a	n/a
26	MAX	chr17:17874901-17876410	Hela-S3	cervix:	n/a	chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876153-17876161 chr17:17876148-17876161 chr17:17876150-17876159 chr17:17876150-17876159
27	POLR2A	chr17:17875346-17875884	Gliobla	brain:	n/a	n/a
28	SIN3AK20	chr17:17875397-17876485	A549	lung:	n/a	n/a
29	POLR2A	chr17:17875305-17876477	H1-neurons	neurons:	n/a	n/a
30	CTCF	chr17:17875260-17875410	AG04449	skin:	n/a	n/a
31	TAF1	chr17:17875332-17876067	ECC-1	luminal epithelium:	n/a	n/a
32	CHD2	chr17:17875012-17876349	Hela-S3	cervix:	n/a	n/a
33	HDAC2	chr17:17875068-17875952	MCF-7	breast:	n/a	n/a
34	POLR2A	chr17:17875338-17875979	HepG2	liver:	n/a	n/a
35	SP1	chr17:17875309-17876559	HCT-116	colon:	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
36	POLR2A	chr17:17874988-17875848	Hela-S3	cervix:	n/a	n/a
37	FOXP2	chr17:17875256-17876013	PFSK-1	brain:	n/a	n/a
38	SP1	chr17:17875308-17876626	HCT-116	colon:	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
39	POLR2A	chr17:17875302-17875993	HUVEC	blood vessel:	n/a	n/a
40	SP1	chr17:17875356-17876498	A549	lung:	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
41	HMGN3	chr17:17875242-17875938	K562	blood:	n/a	n/a
42	SIN3A	chr17:17875377-17876499	H1-hESC	embryonic stem cell:	n/a	chr17:17876149-17876158 chr17:17876151-17876160
43	PBX3	chr17:17875379-17876506	SK-N-SH	brain:	n/a	n/a
44	SIN3AK20	chr17:17875324-17876513	SK-N-SH	brain:	n/a	n/a
45	CTCF	chr17:17875340-17875490	GM12871	blood:	n/a	n/a
46	RFX5	chr17:17874738-17876742	SK-N-SH	brain:	n/a	chr17:17876199-17876208 chr17:17876197-17876211 chr17:17876196-17876211
47	POLR2A	chr17:17874928-17875413	Hela-S3	cervix:	n/a	n/a
48	MXI1	chr17:17875393-17876615	GM12878	blood:	n/a	chr17:17876149-17876158
49	POLR2A	chr17:17875349-17875914	GM12878	blood:	n/a	n/a
50	REST	chr17:17874935-17876422	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:17874682..17878997-chr17:17883276..17886236,4	MCF-7	breast:
2	chr17:17868830..17871208-chr17:17873732..17875523,2	K562	blood:
3	chr17:17868065..17872323-chr17:17872969..17875651,4	MCF-7	breast:

Variant related genes	Relation type
LRRC48	TF binding region
ENSG00000230273	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11078408	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11078409	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11650021	0.81[ASN][1000 genomes]
rs11870660	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12150369	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12600546	0.80[EUR][1000 genomes]
rs12939020	0.81[ASN][1000 genomes]
rs28537385	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2955355	0.81[ASN][1000 genomes]
rs2955356	0.81[ASN][1000 genomes]
rs2955357	0.81[ASN][1000 genomes]
rs2955358	0.81[ASN][1000 genomes]
rs2955383	0.81[ASN][1000 genomes]
rs4299203	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4365348	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4368210	0.84[AMR][1000 genomes]
rs4413022	0.81[AMR][1000 genomes]
rs4459604	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4471742	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4506969	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4584886	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4643387	0.81[ASN][1000 genomes]
rs4924832	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4925133	0.88[EUR][1000 genomes]
rs4925136	0.81[ASN][1000 genomes]
rs57728924	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62064158	0.80[EUR][1000 genomes]
rs62072050	0.80[EUR][1000 genomes]
rs6502631	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6502632	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7207821	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7209003	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7210400	0.81[ASN][1000 genomes]
rs7212167	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7219320	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7223696	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8068175	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8068820	0.80[EUR][1000 genomes]
rs8069811	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8071238	0.82[AMR][1000 genomes]
rs8075189	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8080823	0.80[AMR][1000 genomes]
rs8082590	0.81[ASN][1000 genomes]
rs9897761	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9911850	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9912096	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9913277	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9914127	0.92[AMR][1000 genomes];0.96[EUR][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

No data

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	chr17:17874800-17875600	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr17:17874800-17876400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:17874800-17876400	Active TSS	NHLF	lung
16	chr17:17874800-17876600	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr17:17874800-17876600	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr17:17874800-17876600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr17:17874800-17876600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr17:17874800-17876600	Active TSS	Ovary	ovary
21	chr17:17874800-17876600	Active TSS	HSMMtube	muscle
22	chr17:17874800-17876800	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr17:17874800-17877000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr17:17875000-17876200	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr17:17875000-17876200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr17:17875000-17876200	Active TSS	HepG2	liver
27	chr17:17875000-17876400	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr17:17875000-17876400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr17:17875000-17876400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr17:17875000-17876400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr17:17875000-17876400	Active TSS	Brain Anterior Caudate	brain
32	chr17:17875000-17876400	Active TSS	Rectal Smooth Muscle	rectum
33	chr17:17875000-17876400	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr17:17875000-17876400	Active TSS	Small Intestine	intestine
35	chr17:17875000-17876400	Active TSS	Stomach Mucosa	stomach
36	chr17:17875000-17876400	Active TSS	Hela-S3	cervix
37	chr17:17875000-17876400	Active TSS	HMEC	breast
38	chr17:17875000-17876400	Active TSS	NH-A	brain
39	chr17:17875000-17876400	Active TSS	NHEK	skin
40	chr17:17875000-17876400	Active TSS	Osteobl	bone
41	chr17:17875000-17876600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr17:17875000-17876600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr17:17875000-17876600	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr17:17875000-17876600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr17:17875000-17876600	Active TSS	Muscle Satellite Cultured Cells	--
46	chr17:17875000-17876600	Active TSS	Colon Smooth Muscle	Colon
47	chr17:17875000-17876600	Active TSS	Fetal Intestine Small	intestine
48	chr17:17875000-17876600	Active TSS	Right Ventricle	heart
49	chr17:17875000-17876800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr17:17875000-17876800	Active TSS	H9 Cell Line	embryonic stem cell

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