Variant report

Variant	rs1197701
Chromosome Location	chr15:42187492-42187493
allele	C/T
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	POLR2A	chr15:42187483-42187608	H1-hESC	embryonic stem cell:	n/a	n/a
2	ELF1	chr15:42186391-42187918	GM12878	blood:	n/a	chr15:42186941-42186953
3	POLR2A	chr15:42187055-42187940	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:42187316-42187727	U87	brain:	n/a	n/a
5	POLR2A	chr15:42186852-42187767	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:42186736-42187992	PANC-1	pancreas:	n/a	n/a
7	ZNF263	chr15:42186114-42187973	HEK293-T-REx	kidney:	n/a	chr15:42186877-42186886
8	TCF7L2	chr15:42186906-42187657	HCT-116	colon:	n/a	chr15:42187116-42187125
9	POLR2A	chr15:42186840-42187880	PANC-1	pancreas:	n/a	n/a
10	FOXP2	chr15:42186918-42187643	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr15:42184705-42187956	ECC-1	luminal epithelium:	n/a	n/a
12	RAD21	chr15:42187337-42187749	SK-N-SH_RA	brain:	n/a	n/a
13	POLR2A	chr15:42186890-42188019	GM12878	blood:	n/a	n/a
14	TCF12	chr15:42185817-42187923	ECC-1	luminal epithelium:	n/a	n/a
15	EP300	chr15:42185396-42188142	SK-N-SH	brain:	n/a	chr15:42187116-42187125
16	SRF	chr15:42186870-42187606	ECC-1	luminal epithelium:	n/a	n/a
17	YY1	chr15:42186879-42187690	ECC-1	luminal epithelium:	n/a	chr15:42187135-42187149
18	NFIC	chr15:42183898-42187893	ECC-1	luminal epithelium:	n/a	chr15:42184240-42184268
19	FOS	chr15:42187018-42187538	MCF10A-Er-Src	breast:	n/a	chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125 chr15:42187115-42187126
20	POLR2A	chr15:42187322-42187727	U87	brain:	n/a	n/a
21	MXI1	chr15:42186710-42188078	SK-N-SH	brain:	n/a	n/a
22	NFIC	chr15:42186868-42187945	SK-N-SH	brain:	n/a	n/a
23	EP300	chr15:42186937-42187720	ECC-1	luminal epithelium:	n/a	chr15:42187116-42187125
24	NFIC	chr15:42186771-42187861	ECC-1	luminal epithelium:	n/a	n/a
25	PML	chr15:42186922-42187609	GM12878	blood:	n/a	chr15:42187115-42187124
26	POLR2A	chr15:42186956-42187683	HCT-116	colon:	n/a	n/a
27	SPI1	chr15:42186883-42187592	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:42186930-42187654	GM12878	blood:	n/a	n/a
29	ZBTB7A	chr15:42184792-42187816	ECC-1	luminal epithelium:	n/a	chr15:42186860-42186871 chr15:42185909-42185917
30	MAX	chr15:42186918-42187745	ECC-1	luminal epithelium:	n/a	chr15:42187116-42187125
31	POLR2A	chr15:42186648-42187610	Hela-S3	cervix:	n/a	n/a
32	TCF12	chr15:42186001-42187847	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr15:42186950-42187835	SK-N-SH	brain:	n/a	n/a
34	EP300	chr15:42186946-42187653	SK-N-SH_RA	brain:	n/a	chr15:42187116-42187125
35	JUND	chr15:42186604-42188737	SK-N-SH	brain:	n/a	chr15:42187115-42187126 chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125
36	FOSL2	chr15:42186775-42187769	SK-N-SH	brain:	n/a	chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125
37	MAX	chr15:42186807-42187813	ECC-1	luminal epithelium:	n/a	chr15:42187116-42187125
38	POLR2A	chr15:42186000-42187750	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr15:42185991-42189010	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr15:42186959-42187687	HCT-116	colon:	n/a	n/a
41	CEBPB	chr15:42187373-42187588	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr15:42186929-42188001	GM19193	blood:	n/a	n/a
43	POLR2A	chr15:42186381-42187786	HUVEC	blood vessel:	n/a	n/a
44	MYC	chr15:42186883-42187596	NB4	blood:	n/a	chr15:42187116-42187125
45	BRCA1	chr15:42187447-42187552	HepG2	liver:	n/a	n/a
46	POLR2A	chr15:42187438-42187933	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:42187009-42187616	GM12891	blood:	n/a	n/a
48	RAD21	chr15:42186821-42187738	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr15:42185834-42189791	HUVEC	blood vessel:	n/a	n/a
50	STAT5A	chr15:42186701-42187716	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JMJD7-PLA2G4B-1	chr15:42184991-42187534	ENSG00000174171.3
2	lnc-JMJD7-PLA2G4B-1	chr15:42187183-42188141	ENSG00000174171.3
3	lnc-JMJD7-PLA2G4B-1	chr15:42187383-42187534	ENSG00000174171.3

Variant related genes	Relation type
SPTBN5	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12708402	0.90[CEU][hapmap]
rs2271283	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv517631	chr15:42096926-42187492	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1197701	SPTBN5	cis	Artery Aorta	GTEx
rs1197701	SPTBN5	cis	cerebellar cortex	BrainEAC
rs1197701	SPTBN5	cis	lung	GTEx
rs1197701	SPTBN5	cis	cerebellum	SCAN
rs1197701	BUB1B	cis	cerebellum	SCAN
rs1197701	SPTBN5	cis	Artery Tibial	GTEx
rs1197701	MAPKBP1	cis	cerebellum	SCAN

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	chr15:42183800-42187600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr15:42183800-42195800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:42184000-42188000	Enhancers	Fetal Heart	heart
12	chr15:42184400-42188000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:42184400-42189600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:42184400-42192800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:42184600-42187600	Enhancers	Colon Smooth Muscle	Colon
16	chr15:42184600-42187800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:42184600-42188000	Enhancers	Primary B cells from cord blood	blood
18	chr15:42184600-42188000	Enhancers	Primary hematopoietic stem cells	blood
19	chr15:42184600-42188000	Enhancers	Fetal Stomach	stomach
20	chr15:42184600-42188000	Enhancers	Fetal Thymus	thymus
21	chr15:42184800-42187600	Enhancers	Stomach Mucosa	stomach
22	chr15:42184800-42187800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr15:42185000-42187600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:42185000-42187600	Enhancers	Fetal Intestine Small	intestine
25	chr15:42185000-42187600	Enhancers	Gastric	stomach
26	chr15:42185000-42187800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr15:42185000-42187800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr15:42185400-42188000	Enhancers	Pancreas	Pancrea
29	chr15:42185600-42187600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr15:42185600-42188000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:42185600-42188000	Enhancers	NH-A	brain
32	chr15:42186000-42187600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:42186000-42187600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr15:42186000-42188000	Enhancers	Lung	lung
35	chr15:42186200-42187600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:42186200-42187600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:42186200-42187600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr15:42186200-42187600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:42186200-42187600	Enhancers	Placenta	Placenta
40	chr15:42186200-42187600	Enhancers	Ovary	ovary
41	chr15:42186200-42187600	Enhancers	NHDF-Ad	bronchial
42	chr15:42186200-42188000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:42186200-42192800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:42186400-42187600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr15:42186400-42187600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr15:42186400-42188000	Enhancers	HUVEC	blood vessel
47	chr15:42186600-42187600	Enhancers	H1 Cell Line	embryonic stem cell
48	chr15:42186600-42187600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr15:42186600-42187600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr15:42186600-42187600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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