Variant report

Variant	rs11638797
Chromosome Location	chr15:30062171-30062172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
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];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632848	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11633069	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634700	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636849	0.83[LWK][hapmap];0.83[YRI][hapmap]
rs11637683	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901062	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955758	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]
rs1719031	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851520	0.90[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];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]
rs41280056	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45449102	0.83[ASN][1000 genomes]
rs45474401	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45478093	0.83[ASN][1000 genomes]
rs45505092	0.83[AFR][1000 genomes];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	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307541	0.90[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	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719067	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719069	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719076	0.87[AFR][1000 genomes];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	0.91[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
rs11638797	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	chr15:30021400-30097200	Weak transcription	Aorta	Aorta
3	chr15:30025200-30065000	Weak transcription	Fetal Brain Female	brain
4	chr15:30030400-30067000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:30044600-30064000	Strong transcription	Fetal Intestine Large	intestine
6	chr15:30046400-30064400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:30047000-30065000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:30047000-30066000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:30049400-30066400	Weak transcription	Small Intestine	intestine
10	chr15:30050000-30064000	Strong transcription	Placenta	Placenta
11	chr15:30050200-30070600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:30050400-30064400	Strong transcription	HSMM	muscle
13	chr15:30050600-30063400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:30051400-30063600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:30051600-30065600	Strong transcription	NHEK	skin
16	chr15:30051800-30063800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr15:30052000-30063800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:30052000-30065600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:30052000-30070600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:30052400-30064400	Strong transcription	HUVEC	blood vessel
21	chr15:30052600-30067600	Weak transcription	Stomach Mucosa	stomach
22	chr15:30052600-30089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:30053000-30064600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr15:30053000-30072600	Weak transcription	Spleen	Spleen
25	chr15:30056200-30062200	Strong transcription	HMEC	breast
26	chr15:30056800-30062800	Strong transcription	A549	lung
27	chr15:30057400-30067200	Weak transcription	K562	blood
28	chr15:30057600-30068600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:30058000-30067200	Weak transcription	Psoas Muscle	Psoas
30	chr15:30058200-30062200	Strong transcription	NHDF-Ad	bronchial
31	chr15:30058200-30065600	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:30058200-30067200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:30058400-30062400	Strong transcription	NH-A	brain
34	chr15:30058400-30064400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:30058600-30062200	Weak transcription	Fetal Intestine Small	intestine
36	chr15:30058600-30063200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:30058600-30064400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:30058600-30065600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:30058600-30067200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:30058600-30067200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr15:30058600-30092200	Weak transcription	Esophagus	oesophagus
42	chr15:30058600-30106000	Weak transcription	Gastric	stomach
43	chr15:30059000-30064400	Strong transcription	Osteobl	bone
44	chr15:30059400-30065600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:30059800-30063000	Strong transcription	Fetal Lung	lung
46	chr15:30059800-30063200	Weak transcription	Brain Angular Gyrus	brain
47	chr15:30059800-30063200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr15:30059800-30086200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:30060400-30063600	Weak transcription	Brain Substantia Nigra	brain
50	chr15:30060600-30062200	Strong transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links