Variant report

Variant	rs1672459
Chromosome Location	chr15:42185439-42185440
allele	C/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	POLR2A	chr15:42184705-42187956	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr15:42185396-42188142	SK-N-SH	brain:	n/a	chr15:42187116-42187125
3	NFIC	chr15:42183898-42187893	ECC-1	luminal epithelium:	n/a	chr15:42184240-42184268
4	TCF12	chr15:42183882-42185783	ECC-1	luminal epithelium:	n/a	chr15:42184887-42184894 chr15:42184233-42184240 chr15:42184885-42184895 chr15:42185463-42185470
5	ZBTB7A	chr15:42184792-42187816	ECC-1	luminal epithelium:	n/a	chr15:42186860-42186871 chr15:42185909-42185917
6	NFIC	chr15:42183967-42185460	ECC-1	luminal epithelium:	n/a	chr15:42184240-42184268
7	TCF12	chr15:42183856-42185543	ECC-1	luminal epithelium:	n/a	chr15:42184887-42184894 chr15:42184233-42184240 chr15:42184885-42184895 chr15:42185463-42185470
8	ZBTB7A	chr15:42184766-42187747	ECC-1	luminal epithelium:	n/a	chr15:42186860-42186871 chr15:42185909-42185917
9	EP300	chr15:42183882-42185555	ECC-1	luminal epithelium:	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-2	chr15:42185134-42186566	NONHSAT041977

Variant related genes	Relation type
ENSG00000174171	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1197699	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1618332	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1648815	0.84[AMR][1000 genomes]
rs1704381	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs745646	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	nsv1041645	chr15:42095168-42186482	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv1051733	chr15:42098896-42186482	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	nsv1050892	chr15:42128855-42186482	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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
18	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
19	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
20	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
21	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
22	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
23	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1672459	SPTBN5	cis	Muscle Skeletal	GTEx
rs1672459	EHD4	Cis_1M	lymphoblastoid	RTeQTL
rs1672459	SPTBN5	cis	lung	GTEx
rs1672459	SPTBN5	cis	Adipose Subcutaneous	GTEx
rs1672459	SPTBN5	cis	Artery Aorta	GTEx
rs1672459	SPTBN5	cis	Artery Tibial	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42141200-42191200	Weak transcription	Aorta	Aorta
2	chr15:42174000-42186000	Weak transcription	HSMM	muscle
3	chr15:42174200-42186600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:42175000-42186000	Weak transcription	Adipose Nuclei	Adipose
5	chr15:42175800-42186400	Weak transcription	HUVEC	blood vessel
6	chr15:42175800-42191000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr15:42175800-42191000	Weak transcription	Thymus	Thymus
8	chr15:42178000-42185600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:42181200-42186200	Weak transcription	GM12878-XiMat	blood
10	chr15:42181200-42186600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:42182600-42186200	Weak transcription	Ovary	ovary
12	chr15:42182600-42187800	Enhancers	Fetal Muscle Leg	muscle
13	chr15:42183600-42186200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:42183600-42187000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:42183600-42191200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr15:42183600-42191400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:42183600-42195800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:42183600-42196000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:42183800-42186600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:42183800-42187000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:42183800-42187600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr15:42183800-42195800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:42184000-42185800	Enhancers	Liver	Liver
24	chr15:42184000-42188000	Enhancers	Fetal Heart	heart
25	chr15:42184200-42186000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:42184200-42186800	Enhancers	Primary B cells from peripheral blood	blood
27	chr15:42184400-42188000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:42184400-42189600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:42184400-42192800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:42184600-42185800	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr15:42184600-42186000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:42184600-42186800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:42184600-42187400	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr15:42184600-42187600	Enhancers	Colon Smooth Muscle	Colon
35	chr15:42184600-42187800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:42184600-42188000	Enhancers	Primary B cells from cord blood	blood
37	chr15:42184600-42188000	Enhancers	Primary hematopoietic stem cells	blood
38	chr15:42184600-42188000	Enhancers	Fetal Stomach	stomach
39	chr15:42184600-42188000	Enhancers	Fetal Thymus	thymus
40	chr15:42184800-42185600	Enhancers	Duodenum Mucosa	Duodenum
41	chr15:42184800-42185600	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr15:42184800-42185800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:42184800-42186200	Enhancers	HMEC	breast
44	chr15:42184800-42186600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:42184800-42186800	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr15:42184800-42187000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:42184800-42187600	Enhancers	Stomach Mucosa	stomach
48	chr15:42184800-42187800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr15:42185000-42185600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:42185000-42185800	Active TSS	Left Ventricle	heart

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