Variant report

Variant	rs1715919
Chromosome Location	chr15:56756285-56756286
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56537987..56538847-chr15:56756234..56756979,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF280D-2	chr15:56755978-56756445	NONHSAT044023

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1087837	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11638060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11638076	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11638872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11638965	0.86[ASN][1000 genomes]
rs11639320	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1711483	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17238775	0.81[AMR][1000 genomes]
rs2249183	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs3848113	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705450	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7163544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs72742619	0.82[AMR][1000 genomes]
rs72742631	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72742636	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72742652	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72742667	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72742674	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72742676	0.89[EUR][1000 genomes]
rs72742684	0.81[AMR][1000 genomes]
rs72742686	0.81[AMR][1000 genomes]
rs795781	0.83[ASN][1000 genomes]
rs795785	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs795793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs813267	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1545	chr15:56659498-56897381	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1046891	chr15:56659587-56792033	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv471330	chr15:56659709-56896385	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv471506	chr15:56659709-56896385	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv498847	chr15:56667038-56896395	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2525559	chr15:56669294-56897412	Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv433294	chr15:56676457-56853535	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3693203	chr15:56676457-56894478	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv35150	chr15:56677730-56896304	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv9270	chr15:56686946-56760420	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv2757602	chr15:56736478-56790080	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv2760033	chr15:56736478-56790080	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1715919	MNS1	cis	parietal	SCAN
rs1715919	PXDN	trans	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56716000-56756600	Weak transcription	HSMM	muscle
2	chr15:56723400-56756600	Weak transcription	Fetal Stomach	stomach
3	chr15:56732200-56756800	Weak transcription	Fetal Brain Male	brain
4	chr15:56735200-56756400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:56735400-56756600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:56735600-56756400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:56735600-56756600	Weak transcription	Brain Anterior Caudate	brain
8	chr15:56739600-56756600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:56743200-56756800	Weak transcription	Aorta	Aorta
10	chr15:56744600-56757200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:56747200-56756800	Weak transcription	Stomach Mucosa	stomach
12	chr15:56748000-56756800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:56748600-56756800	Weak transcription	Pancreas	Pancrea
14	chr15:56750200-56756400	Weak transcription	A549	lung
15	chr15:56751000-56756600	Weak transcription	GM12878-XiMat	blood
16	chr15:56751600-56756600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:56754000-56756600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:56754200-56756600	Weak transcription	NH-A	brain
19	chr15:56754600-56756600	Weak transcription	NHLF	lung
20	chr15:56755600-56756600	Enhancers	Fetal Thymus	thymus
21	chr15:56755800-56756400	Weak transcription	HepG2	liver
22	chr15:56755800-56756600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr15:56756000-56756800	Flanking Active TSS	Dnd41	blood
24	chr15:56756000-56757000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr15:56756000-56757800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr15:56756200-56756400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr15:56756200-56756400	Active TSS	Fetal Lung	lung
28	chr15:56756200-56756600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:56756200-56756600	Enhancers	Duodenum Mucosa	Duodenum
30	chr15:56756200-56756600	Enhancers	Osteobl	bone
31	chr15:56756200-56757000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:56756200-56757800	Active TSS	Muscle Satellite Cultured Cells	--
33	chr15:56756200-56757800	Active TSS	K562	blood
34	chr15:56756200-56758000	Active TSS	Fetal Kidney	kidney

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