Variant report

Variant	rs1704381
Chromosome Location	chr15:42188549-42188550
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	POLR2A	chr15:42188357-42190446	GM19193	blood:	n/a	n/a
2	POLR2A	chr15:42188215-42190824	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:42188312-42188762	HCT-116	colon:	n/a	n/a
4	POLR2A	chr15:42188125-42188722	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr15:42188329-42190685	GM12891	blood:	n/a	n/a
6	JUND	chr15:42186604-42188737	SK-N-SH	brain:	n/a	chr15:42187115-42187126 chr15:42187117-42187126 chr15:42187115-42187127 chr15:42187116-42187125
7	POLR2A	chr15:42185991-42189010	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr15:42185834-42189791	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr15:42188353-42188587	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:42188188-42189224	GM12892	blood:	n/a	n/a
11	PML	chr15:42188165-42189060	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:42188283-42189145	GM12892	blood:	n/a	n/a
13	POLR2A	chr15:42188161-42189128	GM12878	blood:	n/a	n/a
14	MTA3	chr15:42188100-42188939	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:42188479-42189241	GM12891	blood:	n/a	n/a
16	POLR2A	chr15:42188291-42190330	GM12878	blood:	n/a	n/a
17	POLR2A	chr15:42188475-42189377	PANC-1	pancreas:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JMJD7-PLA2G4B-2	chr15:42188198-42189719	NONHSAT041984
2	lnc-SPTBN5-3	chr15:42188137-42189031	ENSG00000272003.1

Variant related genes	Relation type
SPTBN5	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1048166	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048175	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1197699	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1648810	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648815	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1672459	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1704386	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1704388	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1704391	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1704396	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1820506	0.83[EUR][1000 genomes]
rs6493011	0.83[AMR][1000 genomes]
rs7183264	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs890502	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1704381	SPTBN5	cis	Adipose Subcutaneous	GTEx
rs1704381	SPTBN5	cis	Artery Tibial	GTEx
rs1704381	EHD4	Cis_1M	lymphoblastoid	RTeQTL
rs1704381	SPTBN5	cis	Artery Aorta	GTEx
rs1704381	SPTBN5	cis	lung	GTEx

Chromatin state (count:102 , 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	chr15:42183600-42191200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:42183600-42191400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:42183600-42195800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:42183600-42196000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:42183800-42195800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42184400-42189600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:42184400-42192800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:42186200-42192800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:42186800-42198800	Weak transcription	Brain Substantia Nigra	brain
13	chr15:42187000-42191200	Weak transcription	Fetal Intestine Large	intestine
14	chr15:42187200-42211800	Weak transcription	Small Intestine	intestine
15	chr15:42187400-42188600	Enhancers	Primary B cells from peripheral blood	blood
16	chr15:42187400-42188800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr15:42187400-42189600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:42187400-42189600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:42187400-42190000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:42187400-42190200	Weak transcription	HSMMtube	muscle
21	chr15:42187400-42191200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:42187400-42191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:42187400-42191200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:42187400-42191600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:42187400-42196600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:42187600-42188800	Weak transcription	Adipose Nuclei	Adipose
27	chr15:42187600-42189000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:42187600-42189000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr15:42187600-42189000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:42187600-42189200	Enhancers	Primary T cells fromperipheralblood	blood
31	chr15:42187600-42189400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:42187600-42189400	Weak transcription	Liver	Liver
33	chr15:42187600-42189400	Weak transcription	NHLF	lung
34	chr15:42187600-42190000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:42187600-42190200	Weak transcription	NHDF-Ad	bronchial
36	chr15:42187600-42190400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:42187600-42190400	Weak transcription	Placenta	Placenta
38	chr15:42187600-42190600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:42187600-42190600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:42187600-42191200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:42187600-42191200	Weak transcription	Osteobl	bone
42	chr15:42187600-42191800	Strong transcription	HSMM	muscle
43	chr15:42187600-42192000	Weak transcription	Ovary	ovary
44	chr15:42187600-42192400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:42187600-42192600	Weak transcription	Colonic Mucosa	Colon
46	chr15:42187600-42192600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:42187600-42192600	Weak transcription	Esophagus	oesophagus
48	chr15:42187600-42192800	Weak transcription	Gastric	stomach
49	chr15:42187600-42192800	Weak transcription	Right Atrium	heart
50	chr15:42187600-42196400	Weak transcription	Brain Hippocampus Middle	brain

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