Variant report

Variant	rs1704380
Chromosome Location	chr15:42187661-42187662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr15:42186391-42187918	GM12878	blood:	n/a	chr15:42186941-42186953
2	POLR2A	chr15:42187055-42187940	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:42187316-42187727	U87	brain:	n/a	n/a
4	POLR2A	chr15:42186852-42187767	GM12892	blood:	n/a	n/a
5	POLR2A	chr15:42186736-42187992	PANC-1	pancreas:	n/a	n/a
6	ZNF263	chr15:42186114-42187973	HEK293-T-REx	kidney:	n/a	chr15:42186877-42186886
7	POLR2A	chr15:42186840-42187880	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr15:42184705-42187956	ECC-1	luminal epithelium:	n/a	n/a
9	RAD21	chr15:42187337-42187749	SK-N-SH_RA	brain:	n/a	n/a
10	POLR2A	chr15:42186890-42188019	GM12878	blood:	n/a	n/a
11	TCF12	chr15:42185817-42187923	ECC-1	luminal epithelium:	n/a	n/a
12	EP300	chr15:42185396-42188142	SK-N-SH	brain:	n/a	chr15:42187116-42187125
13	YY1	chr15:42186879-42187690	ECC-1	luminal epithelium:	n/a	chr15:42187135-42187149
14	NFIC	chr15:42183898-42187893	ECC-1	luminal epithelium:	n/a	chr15:42184240-42184268
15	POLR2A	chr15:42187322-42187727	U87	brain:	n/a	n/a
16	MXI1	chr15:42186710-42188078	SK-N-SH	brain:	n/a	n/a
17	NFIC	chr15:42186868-42187945	SK-N-SH	brain:	n/a	n/a
18	EP300	chr15:42186937-42187720	ECC-1	luminal epithelium:	n/a	chr15:42187116-42187125
19	NFIC	chr15:42186771-42187861	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr15:42186956-42187683	HCT-116	colon:	n/a	n/a
21	ZBTB7A	chr15:42184792-42187816	ECC-1	luminal epithelium:	n/a	chr15:42186860-42186871 chr15:42185909-42185917
22	MAX	chr15:42186918-42187745	ECC-1	luminal epithelium:	n/a	chr15:42187116-42187125
23	TCF12	chr15:42186001-42187847	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr15:42186950-42187835	SK-N-SH	brain:	n/a	n/a
25	JUND	chr15:42186604-42188737	SK-N-SH	brain:	n/a	chr15:42187115-42187126 chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125
26	FOSL2	chr15:42186775-42187769	SK-N-SH	brain:	n/a	chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125
27	MAX	chr15:42186807-42187813	ECC-1	luminal epithelium:	n/a	chr15:42187116-42187125
28	POLR2A	chr15:42186000-42187750	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr15:42185991-42189010	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr15:42186959-42187687	HCT-116	colon:	n/a	n/a
31	POLR2A	chr15:42186929-42188001	GM19193	blood:	n/a	n/a
32	POLR2A	chr15:42186381-42187786	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr15:42187438-42187933	GM12878	blood:	n/a	n/a
34	RAD21	chr15:42186821-42187738	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr15:42185834-42189791	HUVEC	blood vessel:	n/a	n/a
36	STAT5A	chr15:42186701-42187716	GM12878	blood:	n/a	n/a
37	FOS	chr15:42187474-42187666	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr15:42186956-42187922	GM18951	blood:	n/a	n/a
39	POLR2A	chr15:42186874-42187996	GM12892	blood:	n/a	n/a
40	POLR2A	chr15:42186991-42188063	GM12892	blood:	n/a	n/a
41	ZBTB7A	chr15:42184766-42187747	ECC-1	luminal epithelium:	n/a	chr15:42186860-42186871 chr15:42185909-42185917
42	EP300	chr15:42187337-42187684	SK-N-SH_RA	brain:	n/a	n/a
43	TEAD4	chr15:42186832-42187826	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr15:42187613-42187919	H1-hESC	embryonic stem cell:	n/a	n/a
45	EP300	chr15:42185696-42187904	ECC-1	luminal epithelium:	n/a	chr15:42187116-42187125
46	MTA3	chr15:42186717-42188067	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:42186003-42187823	HUVEC	blood vessel:	n/a	n/a
48	TEAD4	chr15:42186799-42187760	ECC-1	luminal epithelium:	n/a	n/a
49	FOS	chr15:42186872-42187981	HUVEC	blood vessel:	n/a	chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125 chr15:42187115-42187126
50	REST	chr15:42187337-42187686	SK-N-SH	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:42187649-42187699	PFSK-1	brain:	n/a
2	chr15:42187649-42187699	MCF-7	breast:	n/a
3	chr15:42187649-42187699	U87	brain:	n/a
4	chr15:42187649-42187699	AG04450	lung:	fetal
5	chr15:42187649-42187699	HAEpiC	amniotic membrane:	n/a
6	chr15:42187649-42187699	HUVEC	blood vessel:	n/a
7	chr15:42187649-42187699	AG04449	skin:	fetal
8	chr15:42187649-42187699	SK-N-MC	brain:	n/a
9	chr15:42187649-42187699	H1-hESC	embryonic stem cell:	embryo
10	chr15:42187649-42187699	IMR90	lung:	fetal
11	chr15:42187649-42187699	K562	blood:	n/a
12	chr15:42187649-42187699	HepG2	liver:	n/a
13	chr15:42187649-42187699	HMEC	breast:	n/a
14	chr15:42187649-42187699	LNCaP	prostate:	n/a
15	chr15:42187649-42187699	MCF10A-Er-Src	breast:	n/a
16	chr15:42187649-42187699	RPTEC	kidney:	n/a
17	chr15:42187649-42187699	SK-N-SH	brain:	n/a
18	chr15:42187649-42187699	NHDF-neo	bronchial:	n/a
19	chr15:42187649-42187699	HRPEpiC	eye:	n/a
20	chr15:42187649-42187699	PrEC	prostate:	n/a
21	chr15:42187649-42187699	PANC-1	pancreas:	n/a
22	chr15:42187649-42187699	SK-N-SH_RA	brain:	n/a
23	chr15:42187649-42187699	HNPCEpiC	eye:	n/a
24	chr15:42187649-42187699	BE2_C	brain:	n/a
25	chr15:42187649-42187699	AG09309	skin:	n/a
26	chr15:42187649-42187699	HRCEpiC	kidney:	n/a
27	chr15:42187649-42187699	ProgFib	skin:	n/a
28	chr15:42187649-42187699	NB4	blood:	n/a
29	chr15:42187649-42187699	HEEpiC	esophagus:	n/a
30	chr15:42187649-42187699	AoSMC	blood vessel:	n/a
31	chr15:42187649-42187699	NT2-D1	testis:	n/a
32	chr15:42187649-42187699	GM12891	blood:	n/a
33	chr15:42187649-42187699	SAEC	small airway:	n/a
34	chr15:42187649-42187699	T-47D	breast:	n/a
35	chr15:42187649-42187699	HCM	heart:	n/a
36	chr15:42187649-42187699	HEK293	kidney:	embryo
37	chr15:42187649-42187699	HRE	kidney:	n/a
38	chr15:42187649-42187699	Jurkat	blood:	n/a
39	chr15:42187649-42187699	Hepatocyte	liver:	n/a
40	chr15:42187649-42187699	ovcar-3	ovarian:	n/a
41	chr15:42187649-42187699	Hela-S3	cervix:	n/a
42	chr15:42187649-42187699	HPAEpiC	pulmonary alveolar:	n/a
43	chr15:42187649-42187699	NH-A	brain:	n/a
44	chr15:42187649-42187699	ECC-1	luminal epithelium:	n/a
45	chr15:42187649-42187699	A549	lung:	n/a
46	chr15:42187649-42187699	HCPEpiC	choroid plexus:	n/a
47	chr15:42187649-42187699	BJ	skin:	n/a
48	chr15:42187649-42187699	GM12878	blood:	n/a
49	chr15:42187649-42187699	GM12892	blood:	n/a
50	chr15:42187649-42187699	Caco-2	colon:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JMJD7-PLA2G4B-1	chr15:42187183-42188141	ENSG00000174171.3

No data

Variant related genes	Relation type
SPTBN5	TF binding region
SPTBN5	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1197683	0.84[ASN][1000 genomes]
rs1197685	0.84[ASN][1000 genomes]
rs1197692	0.84[ASN][1000 genomes]
rs1197697	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1197700	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1201690	0.84[ASN][1000 genomes]
rs1210795	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1038393	chr15:42083574-42188035	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	esv1827003	chr15:42087505-42199076	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1051200	chr15:42095168-42188035	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1036153	chr15:42098896-42188035	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
9	nsv1048606	chr15:42101694-42192760	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
10	nsv904118	chr15:42103822-42207905	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
11	nsv904124	chr15:42109975-42207905	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
12	nsv9244	chr15:42110712-42208805	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
13	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
15	nsv904127	chr15:42142912-42207905	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
16	nsv904128	chr15:42147639-42207905	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
17	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
18	nsv904129	chr15:42162957-42207905	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
19	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42141200-42191200	Weak transcription	Aorta	Aorta
2	chr15:42175800-42191000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:42175800-42191000	Weak transcription	Thymus	Thymus
4	chr15:42182600-42187800	Enhancers	Fetal Muscle Leg	muscle
5	chr15:42183600-42191200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:42183600-42191400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:42183600-42195800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:42183600-42196000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42183800-42195800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:42184000-42188000	Enhancers	Fetal Heart	heart
11	chr15:42184400-42188000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:42184400-42189600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:42184400-42192800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:42184600-42187800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:42184600-42188000	Enhancers	Primary B cells from cord blood	blood
16	chr15:42184600-42188000	Enhancers	Primary hematopoietic stem cells	blood
17	chr15:42184600-42188000	Enhancers	Fetal Stomach	stomach
18	chr15:42184600-42188000	Enhancers	Fetal Thymus	thymus
19	chr15:42184800-42187800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr15:42185000-42187800	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr15:42185000-42187800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr15:42185400-42188000	Enhancers	Pancreas	Pancrea
23	chr15:42185600-42188000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:42185600-42188000	Enhancers	NH-A	brain
25	chr15:42186000-42188000	Enhancers	Lung	lung
26	chr15:42186200-42188000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:42186200-42192800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:42186400-42188000	Enhancers	HUVEC	blood vessel
29	chr15:42186600-42187800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:42186800-42188000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr15:42186800-42198800	Weak transcription	Brain Substantia Nigra	brain
32	chr15:42187000-42188000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr15:42187000-42191200	Weak transcription	Fetal Intestine Large	intestine
34	chr15:42187200-42187800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr15:42187200-42188000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr15:42187200-42211800	Weak transcription	Small Intestine	intestine
37	chr15:42187400-42187800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:42187400-42187800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr15:42187400-42188000	Enhancers	Fetal Muscle Trunk	muscle
40	chr15:42187400-42188000	Enhancers	Left Ventricle	heart
41	chr15:42187400-42188000	Enhancers	HMEC	breast
42	chr15:42187400-42188400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:42187400-42188600	Enhancers	Primary B cells from peripheral blood	blood
44	chr15:42187400-42188800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr15:42187400-42189600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:42187400-42189600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:42187400-42190000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr15:42187400-42190200	Weak transcription	HSMMtube	muscle
49	chr15:42187400-42191200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:42187400-42191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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