Variant report

Variant	rs17704159
Chromosome Location	chr15:93142966-93142967
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr15:93142947-93143173	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr15:93142909-93143147	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr15:93142871-93143066	MCF10A-Er-Src	breast:	n/a	n/a
4	CREB1	chr15:93142801-93143164	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93142176..93144157-chr15:93180474..93183283,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf32-1	chr15:93141788-93143767	ENSG00000258676.2

Variant related genes	Relation type
ENSG00000260337	TF binding region
ENSG00000271763	TF binding region
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11074082	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12324337	0.82[ASN][1000 genomes]
rs1390786	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1472372	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17647392	0.83[EUR][1000 genomes]
rs17647569	0.85[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17647665	0.81[AMR][1000 genomes]
rs17647695	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17704035	0.85[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17704052	0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs17704058	0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs2173062	0.90[JPT][hapmap]
rs34301482	0.93[EUR][1000 genomes]
rs4777724	0.84[AMR][1000 genomes]
rs4777727	0.81[AMR][1000 genomes]
rs56839229	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56910829	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59944160	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61557975	1.00[EUR][1000 genomes]
rs7162755	0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs7177194	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7180979	0.81[ASN][1000 genomes]
rs74029112	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs74029123	0.84[AMR][1000 genomes]
rs74029124	0.84[AMR][1000 genomes]
rs74029143	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8026367	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948621	chr15:92688981-93158095	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
4	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
5	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93128400-93152200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:93138400-93143400	Enhancers	HSMMtube	muscle
3	chr15:93139000-93143200	Enhancers	Fetal Muscle Leg	muscle
4	chr15:93139400-93143800	Enhancers	HSMM	muscle
5	chr15:93139400-93159800	Weak transcription	Fetal Lung	lung
6	chr15:93140600-93146600	Weak transcription	Esophagus	oesophagus
7	chr15:93142000-93143000	Enhancers	Right Ventricle	heart
8	chr15:93142000-93143600	Enhancers	Brain Anterior Caudate	brain
9	chr15:93142000-93144800	Enhancers	Brain Angular Gyrus	brain
10	chr15:93142000-93145200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr15:93142000-93145400	Enhancers	Left Ventricle	heart
12	chr15:93142200-93145000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:93142200-93145200	Enhancers	Brain Cingulate Gyrus	brain
14	chr15:93142200-93156400	Weak transcription	Lung	lung
15	chr15:93142200-93160400	Weak transcription	Right Atrium	heart
16	chr15:93142400-93143600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:93142400-93145200	Enhancers	Brain Substantia Nigra	brain
18	chr15:93142400-93145400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:93142400-93152400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:93142600-93143000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr15:93142600-93143200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:93142600-93143400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr15:93142600-93143600	Enhancers	NH-A	brain
24	chr15:93142600-93145000	Enhancers	Brain Hippocampus Middle	brain
25	chr15:93142800-93143200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:93142800-93143200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:93142800-93143400	Enhancers	Osteobl	bone

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