Variant report

Variant	rs260540
Chromosome Location	chr15:29980501-29980502
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	chr15:29978882..29981352-chr15:29982247..29985034,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10775231	1.00[JPT][hapmap]
rs11636849	1.00[JPT][hapmap]
rs1585900	1.00[JPT][hapmap]
rs260541	0.84[AFR][1000 genomes]
rs6495945	1.00[JPT][hapmap]
rs7168919	1.00[JPT][hapmap]
rs7170406	1.00[JPT][hapmap]
rs785446	1.00[JPT][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
rs260540	SNORD116-29	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:29969200-29992000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:29970600-29980600	Weak transcription	Brain Substantia Nigra	brain
3	chr15:29972800-29989200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:29973600-29989600	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:29977800-29980600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:29977800-29996200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:29978000-29983200	Weak transcription	HMEC	breast
8	chr15:29978400-29982800	Weak transcription	NH-A	brain
9	chr15:29978400-29983000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:29978400-29983200	Weak transcription	HSMMtube	muscle
11	chr15:29978400-29990400	Weak transcription	NHLF	lung
12	chr15:29978600-29983200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:29978600-29983200	Weak transcription	HUVEC	blood vessel
14	chr15:29978600-29983200	Weak transcription	Osteobl	bone
15	chr15:29978600-29983400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:29978600-29984800	Weak transcription	NHDF-Ad	bronchial
17	chr15:29978800-29980800	Enhancers	Liver	Liver
18	chr15:29978800-29983200	Weak transcription	HSMM	muscle
19	chr15:29979000-29980800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:29979000-29981000	Enhancers	Fetal Intestine Large	intestine
21	chr15:29979200-29988400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr15:29979400-29981000	Enhancers	Fetal Intestine Small	intestine
23	chr15:29979600-29981600	Enhancers	Esophagus	oesophagus
24	chr15:29979600-29983000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:29979800-29980800	Enhancers	Pancreas	Pancrea
26	chr15:29979800-29980800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr15:29979800-29981400	Enhancers	Gastric	stomach
28	chr15:29979800-29982800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:29979800-29993000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:29980000-29981200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:29980200-29981200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:29980200-29981800	Enhancers	Stomach Mucosa	stomach
33	chr15:29980200-29982600	Weak transcription	A549	lung
34	chr15:29980200-29983000	Weak transcription	HepG2	liver
35	chr15:29980400-29980600	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr15:29980400-29980800	Enhancers	Colonic Mucosa	Colon
37	chr15:29980400-29981400	Enhancers	Rectal Mucosa Donor 29	rectum

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