Variant report

Variant	rs3088159
Chromosome Location	chr15:42190692-42190693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42188215-42190824	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:42189291-42190842	GM12891	blood:	n/a	n/a
3	POLR2A	chr15:42189268-42190861	GM12892	blood:	n/a	n/a
4	PML	chr15:42190351-42190825	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:42189262-42190953	GM12892	blood:	n/a	n/a
6	MTA3	chr15:42190343-42190858	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:42190637-42190827	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:42190404-42190750	GM12891	blood:	n/a	n/a
9	POLR2A	chr15:42189256-42190826	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42179476..42182408-chr15:42189392..42190926,2	K562	blood:
2	chr15:42190524..42192250-chr15:42192419..42194195,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JMJD7-PLA2G4B-2	chr15:42190365-42190773	ENSG00000260556.1
2	lnc-JMJD7-PLA2G4B-2	chr15:42190365-42191029	NONHSAT041980
3	lnc-JMJD7-PLA2G4B-2	chr15:42190365-42191025	NONHSAT041984
4	lnc-JMJD7-PLA2G4B-2	chr15:42190365-42190773	ENSG00000174171.4

No data

Variant related genes	Relation type
SPTBN5	TF binding region
ENSG00000272003	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1048166	0.81[CHD][hapmap]
rs10518741	0.81[CHD][hapmap]
rs11636923	0.84[EUR][1000 genomes]
rs1209334	0.89[CHD][hapmap]
rs12708402	0.83[TSI][hapmap]
rs13329244	0.91[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs1672461	0.89[CHD][hapmap]
rs17686769	1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28478297	0.84[EUR][1000 genomes]
rs67310386	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8039061	0.85[EUR][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3088159	SPTBN5	cis	Muscle Skeletal	GTEx
rs3088159	SPTBN5	cis	Artery Aorta	GTEx
rs3088159	SPTBN5	cis	Adipose Subcutaneous	GTEx
rs3088159	MAPKBP1	cis	cerebellum	SCAN
rs3088159	SPTBN5	cis	cerebellum	SCAN
rs3088159	SPTBN5	cis	lung	GTEx
rs3088159	SPTBN5	cis	Esophagus Mucosa	GTEx
rs3088159	ZSCAN29	cis	cerebellum	SCAN
rs3088159	SPTBN5	cis	Esophagus Muscularis	GTEx
rs3088159	SPTBN5	cis	Artery Tibial	GTEx
rs3088159	EHD4	Cis_1M	lymphoblastoid	RTeQTL
rs3088159	BUB1B	cis	cerebellum	SCAN
rs3088159	SPTBN5	cis	Thyroid	GTEx

Chromatin state (count:108 , 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	chr15:42184400-42192800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:42186200-42192800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:42186800-42198800	Weak transcription	Brain Substantia Nigra	brain
12	chr15:42187000-42191200	Weak transcription	Fetal Intestine Large	intestine
13	chr15:42187200-42211800	Weak transcription	Small Intestine	intestine
14	chr15:42187400-42191200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:42187400-42191200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:42187400-42191200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:42187400-42191600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr15:42187400-42196600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:42187600-42191200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:42187600-42191200	Weak transcription	Osteobl	bone
21	chr15:42187600-42191800	Strong transcription	HSMM	muscle
22	chr15:42187600-42192000	Weak transcription	Ovary	ovary
23	chr15:42187600-42192400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:42187600-42192600	Weak transcription	Colonic Mucosa	Colon
25	chr15:42187600-42192600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr15:42187600-42192600	Weak transcription	Esophagus	oesophagus
27	chr15:42187600-42192800	Weak transcription	Gastric	stomach
28	chr15:42187600-42192800	Weak transcription	Right Atrium	heart
29	chr15:42187600-42196400	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:42187600-42196600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:42187600-42196600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:42187600-42198800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:42187600-42200400	Weak transcription	Stomach Mucosa	stomach
34	chr15:42187600-42200600	Weak transcription	HepG2	liver
35	chr15:42187600-42209800	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:42187800-42191200	Weak transcription	Spleen	Spleen
37	chr15:42187800-42192000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:42187800-42192200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr15:42187800-42196200	Weak transcription	Brain Angular Gyrus	brain
40	chr15:42187800-42196400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:42187800-42196600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:42187800-42198000	Strong transcription	Fetal Intestine Small	intestine
43	chr15:42187800-42206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:42188000-42191200	Weak transcription	Primary B cells from cord blood	blood
45	chr15:42188000-42191200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr15:42188000-42191200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:42188000-42191200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr15:42188000-42191200	Weak transcription	GM12878-XiMat	blood
49	chr15:42188000-42191400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:42188000-42191800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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