Variant report

Variant	rs260526
Chromosome Location	chr15:29994474-29994475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:29993453..29996171-chr15:29998499..30000876,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11632546	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632848	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11633069	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634700	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636849	0.88[LWK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs11637683	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901062	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955758	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]
rs1719031	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851520	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41280056	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45449102	0.83[ASN][1000 genomes]
rs45474401	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45478093	0.83[ASN][1000 genomes]
rs45505092	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45537235	0.83[ASN][1000 genomes]
rs45583033	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55845402	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307541	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719046	1.00[ASN][1000 genomes]
rs72719047	1.00[ASN][1000 genomes]
rs72719058	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719067	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719069	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719076	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785444	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785445	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv903747	chr15:29361126-30008977	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs260526	SNORD115-2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29977800-29996200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:29980800-29996400	Weak transcription	Colonic Mucosa	Colon
3	chr15:29981400-29994800	Weak transcription	K562	blood
4	chr15:29981400-29996400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:29983600-29996200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:29983600-29997400	Weak transcription	Stomach Mucosa	stomach
7	chr15:29984000-29995400	Weak transcription	Gastric	stomach
8	chr15:29985600-29996200	Weak transcription	Pancreas	Pancrea
9	chr15:29986400-29996000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:29987000-29999400	Weak transcription	Brain Germinal Matrix	brain
11	chr15:29987200-29994600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:29988000-29996200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:29988600-29996000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:29988800-29997000	Weak transcription	Fetal Heart	heart
15	chr15:29988800-29999400	Weak transcription	Fetal Brain Male	brain
16	chr15:29989000-30014800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:29989200-29995000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:29989200-29999200	Weak transcription	Spleen	Spleen
19	chr15:29989400-29995200	Strong transcription	HSMMtube	muscle
20	chr15:29989600-29997000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:29989600-30002400	Strong transcription	Fetal Muscle Leg	muscle
22	chr15:29989600-30013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:29989600-30021200	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:29989600-30027200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:29989800-29997800	Strong transcription	Brain Hippocampus Middle	brain
26	chr15:29989800-30000600	Strong transcription	Adipose Nuclei	Adipose
27	chr15:29990000-30014200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr15:29990000-30016600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr15:29990200-29998000	Strong transcription	NHEK	skin
30	chr15:29990200-30000600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:29990200-30013600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:29990200-30016200	Strong transcription	Left Ventricle	heart
33	chr15:29990200-30028400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:29990400-29995200	Strong transcription	HMEC	breast
35	chr15:29990400-29996200	Weak transcription	Psoas Muscle	Psoas
36	chr15:29990400-30014200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:29990400-30014400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr15:29990400-30014400	Strong transcription	Placenta	Placenta
39	chr15:29990400-30026400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr15:29990600-29996200	Weak transcription	Fetal Brain Female	brain
41	chr15:29990600-30004800	Strong transcription	Fetal Intestine Large	intestine
42	chr15:29990600-30014200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:29990800-29994600	Weak transcription	Esophagus	oesophagus
44	chr15:29990800-29996800	Strong transcription	Brain Anterior Caudate	brain
45	chr15:29990800-30014400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:29991000-29994800	Weak transcription	Brain Angular Gyrus	brain
47	chr15:29991000-29995400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:29991000-29996200	Weak transcription	Aorta	Aorta
49	chr15:29991000-30014200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:29991200-29995000	Genic enhancers	A549	lung

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