Variant report

Variant	rs2290559
Chromosome Location	chr15:42168400-42168401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42161749..42164625-chr15:42167618..42170271,3	K562	blood:
2	chr15:42165119..42167610-chr15:42168028..42170441,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11638188	0.80[ASN][1000 genomes]
rs1197675	0.91[CEU][hapmap]
rs12708402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12708403	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12902949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905012	0.80[ASN][1000 genomes]
rs1648841	0.91[EUR][1000 genomes]
rs17686769	1.00[JPT][hapmap]
rs17737128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271283	1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2290553	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs890503	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs890509	0.88[CEU][hapmap];0.92[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 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	nsv904115	chr15:42076387-42171483	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS 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
4	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
5	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
6	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
7	esv1816120	chr15:42093384-42171578	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS 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	22 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv904117	chr15:42103822-42184794	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
16	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
17	nsv904123	chr15:42109975-42171483	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
18	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
19	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
20	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
21	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
22	nsv904126	chr15:42132896-42171483	Enhancers Strong transcription Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
23	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
24	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
25	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
26	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
27	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2290559	SPTBN5	cis	Artery Tibial	GTEx
rs2290559	SPTBN5	cis	Adipose Subcutaneous	GTEx
rs2290559	BUB1B	cis	cerebellum	SCAN
rs2290559	SPTBN5	cis	Thyroid	GTEx
rs2290559	SPTBN5	cis	Muscle Skeletal	GTEx
rs2290559	SPTBN5	cis	cerebellum	SCAN
rs2290559	SPTBN5	cis	Esophagus Muscularis	GTEx
rs2290559	RPAP1	cis	parietal	SCAN
rs2290559	MAPKBP1	cis	cerebellum	SCAN
rs2290559	SPTBN5	cis	lung	GTEx
rs2290559	SPTBN5	cis	Artery Aorta	GTEx
rs2290559	ZSCAN29	cis	cerebellum	SCAN
rs2290559	C15orf23	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42138200-42173400	Weak transcription	Right Atrium	heart
2	chr15:42141200-42191200	Weak transcription	Aorta	Aorta
3	chr15:42148200-42174400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:42153200-42168600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:42155800-42168400	Weak transcription	Lung	lung
6	chr15:42157400-42179200	Weak transcription	HSMMtube	muscle
7	chr15:42159400-42168800	Weak transcription	Fetal Intestine Small	intestine
8	chr15:42160200-42172600	Weak transcription	HUVEC	blood vessel
9	chr15:42162400-42168400	Weak transcription	Gastric	stomach
10	chr15:42163200-42174000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:42163600-42169600	Weak transcription	Esophagus	oesophagus
12	chr15:42163600-42173000	Weak transcription	HSMM	muscle
13	chr15:42163800-42170000	Weak transcription	Adipose Nuclei	Adipose
14	chr15:42164600-42171800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:42165400-42184800	Weak transcription	HMEC	breast
16	chr15:42165600-42169000	Weak transcription	Pancreas	Pancrea
17	chr15:42167400-42168600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:42167600-42168400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:42167600-42168400	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:42167800-42169200	Enhancers	Primary B cells from peripheral blood	blood
21	chr15:42168000-42168400	Enhancers	Primary B cells from cord blood	blood
22	chr15:42168200-42168400	Active TSS	Spleen	Spleen
23	chr15:42168200-42168600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:42168200-42172200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr15:42168400-42168600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:42168400-42168600	Enhancers	Fetal Thymus	thymus
27	chr15:42168400-42168600	Flanking Active TSS	Spleen	Spleen
28	chr15:42168400-42168800	Strong transcription	Gastric	stomach
29	chr15:42168400-42169000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:42168400-42170200	Strong transcription	Lung	lung
31	chr15:42168400-42171000	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links