Variant report

Variant	rs680493
Chromosome Location	chr15:41136116-41136117
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	EGR1	chr15:41135984-41137164	HCT-116	colon:	n/a	chr15:41136535-41136549 chr15:41136188-41136198 chr15:41136183-41136196 chr15:41136186-41136195 chr15:41136183-41136196 chr15:41136183-41136196 chr15:41136184-41136198 chr15:41136537-41136547 chr15:41136184-41136195 chr15:41136183-41136196 chr15:41136185-41136195 chr15:41136536-41136550 chr15:41136602-41136611 chr15:41136184-41136195 chr15:41136535-41136548 chr15:41136183-41136197 chr15:41136185-41136195
2	EGR1	chr15:41136071-41136304	GM12878	blood:	n/a	chr15:41136188-41136198 chr15:41136183-41136196 chr15:41136186-41136195 chr15:41136183-41136196 chr15:41136183-41136196 chr15:41136184-41136198 chr15:41136184-41136195 chr15:41136183-41136196 chr15:41136185-41136195 chr15:41136184-41136195 chr15:41136183-41136197 chr15:41136185-41136195
3	SIN3AK20	chr15:41135955-41137422	MCF-7	breast:	n/a	n/a
4	CTBP2	chr15:41135944-41137100	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZEB1	chr15:41136068-41136859	GM12878	blood:	n/a	chr15:41136372-41136379 chr15:41136370-41136379 chr15:41136646-41136657
6	UBTF	chr15:41135902-41136242	K562	blood:	n/a	n/a
7	CHD2	chr15:41136029-41136296	H1-hESC	embryonic stem cell:	n/a	n/a
8	ELF1	chr15:41135827-41137451	GM12878	blood:	n/a	chr15:41136197-41136206 chr15:41136192-41136204 chr15:41135983-41135995
9	NR2F2	chr15:41136099-41136998	MCF-7	breast:	n/a	n/a
10	POLR2A	chr15:41135912-41137071	MCF-7	breast:	n/a	n/a
11	POLR2A	chr15:41135422-41137445	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr15:41135988-41136850	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr15:41136081-41137354	ECC-1	luminal epithelium:	n/a	chr15:41136085-41136101 chr15:41136086-41136102 chr15:41136417-41136433 chr15:41136179-41136195
14	POLR2A	chr15:41135645-41137310	MCF-7	breast:	n/a	n/a
15	TAF1	chr15:41135862-41137255	ECC-1	luminal epithelium:	n/a	n/a
16	HMGN3	chr15:41135940-41136945	K562	blood:	n/a	chr15:41136237-41136246
17	CCNT2	chr15:41135927-41136545	K562	blood:	n/a	n/a
18	POLR2A	chr15:41135866-41136650	K562	blood:	n/a	n/a
19	TAF1	chr15:41135745-41137209	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr15:41135393-41136741	MCF10A-Er-Src	breast:	n/a	n/a
21	SIN3AK20	chr15:41135661-41136335	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr15:41135442-41137369	HCT-116	colon:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
23	MAZ	chr15:41136013-41136637	K562	blood:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
24	POLR2A	chr15:41135995-41137213	H1-hESC	embryonic stem cell:	n/a	n/a
25	TCF12	chr15:41136011-41137345	ECC-1	luminal epithelium:	n/a	n/a
26	EGR1	chr15:41136058-41136651	K562	blood:	n/a	chr15:41136535-41136549 chr15:41136188-41136198 chr15:41136183-41136196 chr15:41136186-41136195 chr15:41136183-41136196 chr15:41136183-41136196 chr15:41136184-41136198 chr15:41136537-41136547 chr15:41136184-41136195 chr15:41136183-41136196 chr15:41136185-41136195 chr15:41136536-41136550 chr15:41136602-41136611 chr15:41136184-41136195 chr15:41136535-41136548 chr15:41136183-41136197 chr15:41136185-41136195
27	TCF7L2	chr15:41136011-41137058	HCT-116	colon:	n/a	chr15:41136446-41136455
28	E2F6	chr15:41136018-41136206	K562	blood:	n/a	chr15:41136192-41136202
29	PAX5	chr15:41136050-41136564	GM12892	blood:	n/a	n/a
30	GABPA	chr15:41135974-41136875	MCF-7	breast:	n/a	chr15:41136188-41136197 chr15:41136396-41136405 chr15:41136040-41136049
31	MYC	chr15:41136077-41136823	MCF10A-Er-Src	breast:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
32	ZNF143	chr15:41136050-41136651	H1-hESC	embryonic stem cell:	n/a	n/a
33	ZEB1	chr15:41135616-41136871	HepG2	liver:	n/a	chr15:41135832-41135843 chr15:41136372-41136379 chr15:41136370-41136379 chr15:41136646-41136657
34	EGR1	chr15:41136052-41136789	ECC-1	luminal epithelium:	n/a	chr15:41136535-41136549 chr15:41136188-41136198 chr15:41136183-41136196 chr15:41136186-41136195 chr15:41136183-41136196 chr15:41136183-41136196 chr15:41136184-41136198 chr15:41136537-41136547 chr15:41136184-41136195 chr15:41136183-41136196 chr15:41136185-41136195 chr15:41136536-41136550 chr15:41136602-41136611 chr15:41136184-41136195 chr15:41136535-41136548 chr15:41136183-41136197 chr15:41136185-41136195
35	ZBTB7A	chr15:41135746-41137301	ECC-1	luminal epithelium:	n/a	chr15:41136391-41136399
36	TAF1	chr15:41136007-41136665	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr15:41135881-41136738	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr15:41135481-41137236	ECC-1	luminal epithelium:	n/a	n/a
39	ZNF263	chr15:41136025-41136983	HEK293-T-REx	kidney:	n/a	chr15:41136590-41136611 chr15:41136740-41136749 chr15:41136590-41136599
40	ZBTB7A	chr15:41135899-41136429	K562	blood:	n/a	chr15:41136391-41136399
41	EGR1	chr15:41135966-41136781	MCF-7	breast:	n/a	chr15:41136535-41136549 chr15:41136188-41136198 chr15:41136183-41136196 chr15:41136186-41136195 chr15:41136183-41136196 chr15:41136183-41136196 chr15:41136184-41136198 chr15:41136537-41136547 chr15:41136184-41136195 chr15:41136183-41136196 chr15:41136185-41136195 chr15:41136536-41136550 chr15:41136602-41136611 chr15:41136184-41136195 chr15:41136535-41136548 chr15:41136183-41136197 chr15:41136185-41136195
42	ZEB1	chr15:41135490-41137303	GM12878	blood:	n/a	chr15:41135832-41135843 chr15:41136372-41136379 chr15:41136370-41136379 chr15:41136646-41136657
43	POLR2A	chr15:41136066-41136851	H1-hESC	embryonic stem cell:	n/a	n/a
44	TBP	chr15:41136006-41137186	H1-hESC	embryonic stem cell:	n/a	n/a
45	GABPA	chr15:41136047-41136888	MCF-7	breast:	n/a	chr15:41136188-41136197 chr15:41136396-41136405
46	POLR2A	chr15:41135935-41137248	MCF-7	breast:	n/a	n/a
47	POLR2A	chr15:41135853-41136834	HCT-116	colon:	n/a	n/a
48	POLR2A	chr15:41135953-41136882	HCT-116	colon:	n/a	n/a
49	EGR1	chr15:41135911-41136712	H1-hESC	embryonic stem cell:	n/a	chr15:41136535-41136549 chr15:41136188-41136198 chr15:41136183-41136196 chr15:41136186-41136195 chr15:41136183-41136196 chr15:41136183-41136196 chr15:41136184-41136198 chr15:41136537-41136547 chr15:41136184-41136195 chr15:41136183-41136196 chr15:41136185-41136195 chr15:41136536-41136550 chr15:41136602-41136611 chr15:41136184-41136195 chr15:41136535-41136548 chr15:41136183-41136197 chr15:41136185-41136195
50	EGR1	chr15:41136058-41136822	ECC-1	luminal epithelium:	n/a	chr15:41136535-41136549 chr15:41136188-41136198 chr15:41136183-41136196 chr15:41136186-41136195 chr15:41136183-41136196 chr15:41136183-41136196 chr15:41136184-41136198 chr15:41136537-41136547 chr15:41136184-41136195 chr15:41136183-41136196 chr15:41136185-41136195 chr15:41136536-41136550 chr15:41136602-41136611 chr15:41136184-41136195 chr15:41136535-41136548 chr15:41136183-41136197 chr15:41136185-41136195

No.	Distal block	Cell Line	Cell type
1	chr15:41098435..41103357-chr15:41133527..41139132,10	MCF-7	breast:
2	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
3	chr15:41135781..41139367-chr15:41195514..41200270,4	MCF-7	breast:
4	chr15:41135079..41139908-chr15:41161283..41167324,7	MCF-7	breast:
5	chr15:41050847..41052798-chr15:41135268..41136987,2	K562	blood:
6	chr15:41045671..41048162-chr15:41135920..41137784,2	MCF-7	breast:
7	chr15:41120065..41123435-chr15:41135561..41137302,3	MCF-7	breast:
8	chr15:41099271..41102222-chr15:41135281..41137187,2	K562	blood:
9	chr15:41135632..41136132-chr6:117803609..117804174,2	HCT-116	colon:
10	chr15:41098123..41102222-chr15:41134582..41138137,4	K562	blood:
11	chr15:41135103..41140677-chr15:41182913..41189081,12	MCF-7	breast:
12	chr15:41129275..41132805-chr15:41134409..41137816,5	MCF-7	breast:
13	chr15:40985736..40987452-chr15:41134754..41137017,2	MCF-7	breast:
14	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261183	TF binding region
SPINT1	TF binding region
ENSG00000271236	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000166143	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000164465	Chromatin interaction
ENSG00000261183	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11639292	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2291618	0.98[ASN][1000 genomes]
rs2412569	0.99[EUR][1000 genomes]
rs2412570	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2917953	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3759798	0.98[ASN][1000 genomes]
rs59831883	0.95[ASN][1000 genomes]
rs622538	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668708	0.87[EUR][1000 genomes]
rs668750	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs689589	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs689594	0.90[EUR][1000 genomes]
rs689618	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs689733	0.85[EUR][1000 genomes]
rs689736	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs690435	0.90[EUR][1000 genomes]
rs690572	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs690660	0.99[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	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs680493	RP11-111A22.1	cis	Artery Tibial	GTEx
rs680493	C15orf57	cis	Artery Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41135200-41137800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr15:41135200-41138800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:41135200-41139000	Active TSS	Fetal Kidney	kidney
4	chr15:41135400-41137000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:41135400-41137000	Active TSS	Duodenum Mucosa	Duodenum
6	chr15:41135400-41137400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:41135400-41137600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:41135600-41136200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:41135600-41136200	Enhancers	Liver	Liver
10	chr15:41135600-41136200	Bivalent Enhancer	Brain Substantia Nigra	brain
11	chr15:41135600-41136200	Enhancers	Spleen	Spleen
12	chr15:41135600-41136800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:41135600-41136800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr15:41135600-41137200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
15	chr15:41135600-41137200	Flanking Active TSS	Colonic Mucosa	Colon
16	chr15:41135600-41137200	Active TSS	Small Intestine	intestine
17	chr15:41135600-41137400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:41135600-41137400	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:41135600-41137400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr15:41135600-41137600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr15:41135600-41137600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:41135600-41137600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr15:41135600-41137600	Active TSS	Placenta Amnion	Placenta Amnion
24	chr15:41135600-41138200	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr15:41135600-41138400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr15:41135600-41138400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:41135600-41138600	Active TSS	Gastric	stomach
28	chr15:41135600-41140200	Active TSS	Rectal Smooth Muscle	rectum
29	chr15:41135600-41140400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:41135800-41136200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:41135800-41136200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:41135800-41136200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:41135800-41136200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
34	chr15:41135800-41136200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:41135800-41136200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:41135800-41136200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:41135800-41136200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:41135800-41136200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
39	chr15:41135800-41136200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
40	chr15:41135800-41136200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:41135800-41136200	Bivalent/Poised TSS	Fetal Brain Female	brain
42	chr15:41135800-41136200	Bivalent/Poised TSS	Fetal Thymus	thymus
43	chr15:41135800-41136200	Active TSS	Left Ventricle	heart
44	chr15:41135800-41136200	Active TSS	Lung	lung
45	chr15:41135800-41136200	Bivalent/Poised TSS	Psoas Muscle	Psoas
46	chr15:41135800-41136200	Active TSS	Right Atrium	heart
47	chr15:41135800-41136200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
48	chr15:41135800-41136200	Bivalent Enhancer	NHLF	lung
49	chr15:41135800-41136200	Bivalent/Poised TSS	Osteobl	bone
50	chr15:41135800-41136400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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