Variant report

Variant	rs16955758
Chromosome Location	chr15:30059722-30059723
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:30055034..30056765-chr15:30057565..30059785,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11632546	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632848	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11633069	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634700	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637683	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901062	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719031	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851520	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41280056	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45449102	0.83[ASN][1000 genomes]
rs45474401	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45478093	0.83[ASN][1000 genomes]
rs45505092	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45537235	0.83[ASN][1000 genomes]
rs45583033	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55845402	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307541	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719046	1.00[ASN][1000 genomes]
rs72719047	1.00[ASN][1000 genomes]
rs72719058	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719067	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719069	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719076	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785444	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785445	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv832944	chr15:29861062-30082057	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16955758	SNORD115-2	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30016600-30068200	Weak transcription	Brain Germinal Matrix	brain
2	chr15:30021200-30061600	Weak transcription	Colonic Mucosa	Colon
3	chr15:30021400-30097200	Weak transcription	Aorta	Aorta
4	chr15:30025200-30065000	Weak transcription	Fetal Brain Female	brain
5	chr15:30030400-30060800	Weak transcription	Hela-S3	cervix
6	chr15:30030400-30067000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:30042000-30061800	Weak transcription	Pancreas	Pancrea
8	chr15:30044600-30064000	Strong transcription	Fetal Intestine Large	intestine
9	chr15:30046400-30064400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:30047000-30065000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:30047000-30066000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:30049400-30066400	Weak transcription	Small Intestine	intestine
13	chr15:30049600-30061600	Weak transcription	Fetal Brain Male	brain
14	chr15:30050000-30064000	Strong transcription	Placenta	Placenta
15	chr15:30050200-30070600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr15:30050400-30064400	Strong transcription	HSMM	muscle
17	chr15:30050600-30063400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:30051400-30060600	Strong transcription	HepG2	liver
19	chr15:30051400-30063600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:30051600-30065600	Strong transcription	NHEK	skin
21	chr15:30051800-30061800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:30051800-30063800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr15:30052000-30063800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:30052000-30065600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:30052000-30070600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:30052400-30064400	Strong transcription	HUVEC	blood vessel
27	chr15:30052600-30061600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:30052600-30067600	Weak transcription	Stomach Mucosa	stomach
29	chr15:30052600-30089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:30053000-30064600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr15:30053000-30072600	Weak transcription	Spleen	Spleen
32	chr15:30055000-30060600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:30055800-30059800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr15:30056200-30059800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr15:30056200-30060000	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:30056200-30062200	Strong transcription	HMEC	breast
37	chr15:30056800-30059800	Strong transcription	HSMMtube	muscle
38	chr15:30056800-30062800	Strong transcription	A549	lung
39	chr15:30057400-30059800	Genic enhancers	Fetal Lung	lung
40	chr15:30057400-30067200	Weak transcription	K562	blood
41	chr15:30057600-30068600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr15:30057800-30060600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:30057800-30060600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr15:30057800-30060600	Genic enhancers	Left Ventricle	heart
45	chr15:30058000-30060400	Enhancers	Colon Smooth Muscle	Colon
46	chr15:30058000-30060600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:30058000-30061800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr15:30058000-30061800	Weak transcription	Ovary	ovary
49	chr15:30058000-30067200	Weak transcription	Psoas Muscle	Psoas
50	chr15:30058200-30059800	Enhancers	Brain Angular Gyrus	brain

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