Variant report

Variant	rs17516362
Chromosome Location	chr14:21944955-21944956
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:264)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:264 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:21944565-21945671	HepG2	liver:	n/a	n/a
2	STAT3	chr14:21944354-21945450	MCF10A-Er-Src	breast:	n/a	chr14:21945183-21945203 chr14:21945124-21945136 chr14:21945138-21945150
3	YY1	chr14:21944614-21945932	HepG2	liver:	n/a	chr14:21945140-21945151 chr14:21945135-21945146 chr14:21944915-21944924 chr14:21944912-21944921
4	POLR2A	chr14:21944887-21945571	GM10847	blood:	n/a	n/a
5	SP1	chr14:21944410-21945550	HepG2	liver:	n/a	chr14:21944911-21944921 chr14:21945141-21945153 chr14:21945143-21945152 chr14:21944912-21944921 chr14:21945141-21945153 chr14:21944910-21944922 chr14:21944911-21944921 chr14:21945142-21945151 chr14:21945134-21945148 chr14:21944910-21944922 chr14:21944911-21944920 chr14:21945142-21945156 chr14:21944911-21944920
6	ZNF143	chr14:21944935-21945515	K562	blood:	n/a	n/a
7	HMGN3	chr14:21944937-21945507	K562	blood:	n/a	n/a
8	RFX5	chr14:21944568-21945623	HepG2	liver:	n/a	n/a
9	BHLHE40	chr14:21944452-21945654	HepG2	liver:	n/a	n/a
10	REST	chr14:21944508-21945140	HepG2	liver:	n/a	n/a
11	JUND	chr14:21944873-21945576	HepG2	liver:	n/a	chr14:21945136-21945145
12	RUNX3	chr14:21944555-21945735	GM12878	blood:	n/a	n/a
13	STAT3	chr14:21943930-21945603	MCF10A-Er-Src	breast:	n/a	chr14:21945183-21945203 chr14:21945124-21945136 chr14:21945138-21945150
14	TBP	chr14:21944534-21945470	HepG2	liver:	n/a	n/a
15	MTA3	chr14:21944537-21945764	GM12878	blood:	n/a	n/a
16	MXI1	chr14:21943930-21946175	SK-N-SH	brain:	n/a	n/a
17	TAF1	chr14:21944576-21945882	HepG2	liver:	n/a	n/a
18	GATA3	chr14:21944846-21945489	T-47D	breast:	n/a	n/a
19	GABPA	chr14:21944890-21945781	SK-N-SH	brain:	n/a	chr14:21944912-21944921
20	HCFC1	chr14:21944639-21945651	K562	blood:	n/a	n/a
21	POLR2A	chr14:21944543-21945916	K562	blood:	n/a	n/a
22	POLR2A	chr14:21944625-21945637	Gliobla	brain:	n/a	n/a
23	POLR2A	chr14:21944725-21945540	H1-hESC	embryonic stem cell:	n/a	n/a
24	SRF	chr14:21944867-21945409	GM12878	blood:	n/a	chr14:21945143-21945153
25	TAF1	chr14:21944865-21945526	K562	blood:	n/a	n/a
26	MBD4	chr14:21944324-21945006	HepG2	liver:	n/a	n/a
27	POLR2A	chr14:21944677-21945780	GM12892	blood:	n/a	n/a
28	POLR2A	chr14:21944876-21945123	SK-N-SH	brain:	n/a	n/a
29	CEBPD	chr14:21944588-21945641	HepG2	liver:	n/a	n/a
30	POLR2A	chr14:21944556-21945621	K562	blood:	n/a	n/a
31	POLR2A	chr14:21944539-21945549	HCT-116	colon:	n/a	n/a
32	MXI1	chr14:21944519-21945655	Hela-S3	cervix:	n/a	n/a
33	RUNX3	chr14:21944471-21945587	GM12878	blood:	n/a	n/a
34	GABPA	chr14:21944471-21945884	MCF-7	breast:	n/a	chr14:21944912-21944921
35	POLR2A	chr14:21944630-21945731	GM19193	blood:	n/a	n/a
36	SIN3AK20	chr14:21944379-21945978	MCF-7	breast:	n/a	n/a
37	ZNF143	chr14:21944718-21945541	Hela-S3	cervix:	n/a	n/a
38	MAZ	chr14:21944485-21945757	GM12878	blood:	n/a	chr14:21944916-21944926
39	POLR2A	chr14:21944867-21945140	HepG2	liver:	n/a	n/a
40	ATF2	chr14:21944895-21945496	GM12878	blood:	n/a	n/a
41	POLR2A	chr14:21944625-21945625	GM15510	blood:	n/a	n/a
42	NFYB	chr14:21944932-21945640	GM12878	blood:	n/a	n/a
43	POLR2A	chr14:21944919-21945114	A549	lung:	n/a	n/a
44	POLR2A	chr14:21944624-21945742	HL-60	blood:	n/a	n/a
45	ZNF143	chr14:21944633-21945641	GM12878	blood:	n/a	n/a
46	GABPA	chr14:21944914-21945807	HL-60	blood:	n/a	n/a
47	POLR2A	chr14:21944894-21945600	GM12892	blood:	n/a	n/a
48	TAF1	chr14:21944534-21945633	ECC-1	luminal epithelium:	n/a	n/a
49	JUND	chr14:21944514-21945563	A549	lung:	n/a	chr14:21945136-21945145
50	CREB1	chr14:21944779-21945828	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr14:21944942-21944992	PANC-1	pancreas:	n/a
2	chr14:21944942-21944992	IMR90	lung:	fetal
3	chr14:21944942-21944992	RPTEC	kidney:	n/a
4	chr14:21944942-21944992	HRCEpiC	kidney:	n/a
5	chr14:21944942-21944992	T-47D	breast:	n/a
6	chr14:21944942-21944992	ECC-1	luminal epithelium:	n/a
7	chr14:21944942-21944992	LNCaP	prostate:	n/a
8	chr14:21944942-21944992	HNPCEpiC	eye:	n/a
9	chr14:21944942-21944992	AG04450	lung:	fetal
10	chr14:21944942-21944992	HCPEpiC	choroid plexus:	n/a
11	chr14:21944942-21944992	HRPEpiC	eye:	n/a
12	chr14:21944942-21944992	AoSMC	blood vessel:	n/a
13	chr14:21944942-21944992	NT2-D1	testis:	n/a
14	chr14:21944942-21944992	HCM	heart:	n/a
15	chr14:21944942-21944992	HPAEpiC	pulmonary alveolar:	n/a
16	chr14:21944942-21944992	SKMC	muscle:	n/a
17	chr14:21944942-21944992	BJ	skin:	n/a
18	chr14:21944942-21944992	SK-N-MC	brain:	n/a
19	chr14:21944942-21944992	HEEpiC	esophagus:	n/a
20	chr14:21944942-21944992	Jurkat	blood:	n/a
21	chr14:21944942-21944992	HMEC	breast:	n/a
22	chr14:21944942-21944992	PFSK-1	brain:	n/a
23	chr14:21944942-21944992	MCF-7	breast:	n/a
24	chr14:21944942-21944992	ovcar-3	ovarian:	n/a
25	chr14:21944942-21944992	AG10803	skin:	n/a
26	chr14:21944942-21944992	NB4	blood:	n/a
27	chr14:21944942-21944992	H1-hESC	embryonic stem cell:	embryo
28	chr14:21944942-21944992	Hela-S3	cervix:	n/a
29	chr14:21944942-21944992	U87	brain:	n/a
30	chr14:21944942-21944992	GM06990	blood:	n/a
31	chr14:21944942-21944992	HEK293	kidney:	embryo
32	chr14:21944942-21944992	NH-A	brain:	n/a
33	chr14:21944942-21944992	A549	lung:	n/a
34	chr14:21944942-21944992	NHDF-neo	bronchial:	n/a
35	chr14:21944942-21944992	HRE	kidney:	n/a
36	chr14:21944942-21944992	K562	blood:	n/a
37	chr14:21944942-21944992	MCF10A-Er-Src	breast:	n/a
38	chr14:21944942-21944992	PrEC	prostate:	n/a
39	chr14:21944942-21944992	SK-N-SH	brain:	n/a
40	chr14:21944942-21944992	GM12892	blood:	n/a
41	chr14:21944942-21944992	SK-N-SH_RA	brain:	n/a
42	chr14:21944942-21944992	GM19239	blood:	n/a
43	chr14:21944942-21944992	HepG2	liver:	n/a
44	chr14:21944942-21944992	CMK	blood:	n/a
45	chr14:21944942-21944992	GM12878	blood:	n/a
46	chr14:21944942-21944992	HL-60	blood:	n/a
47	chr14:21944942-21944992	HIPEpiC	eye:	n/a
48	chr14:21944942-21944992	HCF	heart:	n/a
49	chr14:21944942-21944992	HAEpiC	amniotic membrane:	n/a
50	chr14:21944942-21944992	Hepatocyte	liver:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:21944743..21947528-chr14:21994092..21996767,2	MCF-7	breast:
2	chr14:21923260..21925455-chr14:21943748..21947334,4	K562	blood:
3	chr14:21943182..21946742-chr14:21976824..21981257,10	MCF-7	breast:
4	chr14:21903784..21905572-chr14:21943555..21945925,2	MCF-7	breast:
5	chr14:21922721..21925394-chr14:21943917..21947287,10	MCF-7	breast:
6	chr1:149858313..149859863-chr14:21943720..21946355,2	MCF-7	breast:
7	chr14:21903666..21907303-chr14:21944223..21946943,4	K562	blood:
8	chr14:21922608..21930261-chr14:21941288..21947915,21	MCF-7	breast:
9	chr14:21943174..21947446-chr14:21976603..21980796,8	K562	blood:
10	chr14:21943699..21946735-chr14:21977733..21982256,4	MCF-7	breast:
11	chr14:21944239..21947571-chr14:21970430..21973821,4	MCF-7	breast:
12	chr14:21941797..21947093-chr14:21954513..21961521,11	MCF-7	breast:

No data

Variant related genes	Relation type
RAB2B	TF binding region
TOX4	TF binding region
RAB2B	CpG island
TOX4	CpG island
ENSG00000092203	Chromatin interaction
ENSG00000165821	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000100888	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000165819	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10450907	0.90[EUR][1000 genomes]
rs10450908	0.89[EUR][1000 genomes]
rs1061027	0.90[EUR][1000 genomes]
rs11850178	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11852218	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13329035	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3168880	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3762163	0.83[EUR][1000 genomes]
rs55690316	0.90[EUR][1000 genomes]
rs58901398	0.83[EUR][1000 genomes]
rs61973218	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61973219	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61973220	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61973223	0.92[EUR][1000 genomes]
rs66771279	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs719785	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
2	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	esv3518898	chr14:21805983-22077584	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	esv3518899	chr14:21805983-22077584	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1054013	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv541991	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv530011	chr14:21876973-21985341	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv2422459	chr14:21931624-22169502	Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17516362	TOX4	Cis_1M	lymphoblastoid	RTeQTL
rs17516362	RAB2B	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21943800-21946000	Active TSS	Brain Anterior Caudate	brain
2	chr14:21943800-21946000	Active TSS	Rectal Smooth Muscle	rectum
3	chr14:21943800-21946400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr14:21943800-21946400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:21943800-21946600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr14:21943800-21946800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr14:21943800-21946800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr14:21943800-21946800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr14:21944000-21945800	Active TSS	Colonic Mucosa	Colon
10	chr14:21944000-21946000	Active TSS	Esophagus	oesophagus
11	chr14:21944000-21946000	Active TSS	Fetal Brain Male	brain
12	chr14:21944000-21946200	Active TSS	Lung	lung
13	chr14:21944000-21946200	Active TSS	Right Atrium	heart
14	chr14:21944000-21946400	Active TSS	K562	blood
15	chr14:21944000-21946800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr14:21944200-21945400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr14:21944200-21945400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr14:21944200-21945400	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr14:21944200-21945600	Active TSS	Primary T cells fromperipheralblood	blood
20	chr14:21944200-21946000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr14:21944200-21946000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr14:21944200-21946000	Active TSS	Placenta	Placenta
23	chr14:21944200-21946000	Active TSS	Placenta Amnion	Placenta Amnion
24	chr14:21944200-21946000	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr14:21944200-21946000	Active TSS	Stomach Smooth Muscle	stomach
26	chr14:21944200-21946200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr14:21944200-21946200	Active TSS	Muscle Satellite Cultured Cells	--
28	chr14:21944200-21946200	Active TSS	Fetal Intestine Large	intestine
29	chr14:21944200-21946200	Active TSS	Pancreas	Pancrea
30	chr14:21944200-21946200	Active TSS	Thymus	Thymus
31	chr14:21944200-21946200	Bivalent/Poised TSS	HepG2	liver
32	chr14:21944200-21946400	Active TSS	H9 Cell Line	embryonic stem cell
33	chr14:21944200-21946400	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr14:21944200-21946400	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr14:21944200-21946400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr14:21944200-21946400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr14:21944200-21946400	Active TSS	Fetal Thymus	thymus
38	chr14:21944200-21946400	Active TSS	A549	lung
39	chr14:21944200-21946600	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr14:21944200-21946600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr14:21944200-21946600	Active TSS	Fetal Intestine Small	intestine
42	chr14:21944200-21946600	Active TSS	Fetal Kidney	kidney
43	chr14:21944200-21946800	Active TSS	HMEC	breast
44	chr14:21944200-21946800	Active TSS	NHDF-Ad	bronchial
45	chr14:21944200-21946800	Active TSS	NHLF	lung
46	chr14:21944200-21947000	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr14:21944400-21945800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr14:21944400-21945800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr14:21944400-21945800	Active TSS	Liver	Liver
50	chr14:21944400-21945800	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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