Variant report

Variant	rs7178007
Chromosome Location	chr15:78965254-78965255
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	chr15:78963944..78966069-chr3:64562152..64564273,2	MCF-7	breast:
2	chr15:78963617..78966292-chr15:78967103..78969117,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12324870	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12901241	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12905273	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12905641	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910237	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915539	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28444683	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34275594	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34694149	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35701817	0.83[AMR][1000 genomes]
rs35704045	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58946838	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61630816	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62010555	0.83[AMR][1000 genomes]
rs7169223	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8038920	0.90[EUR][1000 genomes]
rs922691	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv974713	chr15:78945824-78996783	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv457209	chr15:78949127-78986805	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv471256	chr15:78949127-78986805	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv570203	chr15:78949127-78986805	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7178007	CHRNA5	cis	Muscle Skeletal	GTEx
rs7178007	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78963600-78965400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:78963600-78965600	Enhancers	Fetal Lung	lung
3	chr15:78963600-78966000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
4	chr15:78963600-78966200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:78963600-78966600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr15:78963800-78965400	Enhancers	Esophagus	oesophagus
7	chr15:78963800-78966000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr15:78963800-78966000	Enhancers	Adipose Nuclei	Adipose
9	chr15:78963800-78966000	Enhancers	Fetal Muscle Leg	muscle
10	chr15:78963800-78966400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr15:78964000-78965400	Enhancers	Fetal Stomach	stomach
12	chr15:78964000-78966600	Enhancers	Spleen	Spleen
13	chr15:78964000-78966800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr15:78964200-78965400	Enhancers	HepG2	liver
15	chr15:78964200-78965600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:78964200-78965600	Enhancers	Brain Anterior Caudate	brain
17	chr15:78964200-78965600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr15:78964200-78965600	Enhancers	HSMMtube	muscle
19	chr15:78964200-78966000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:78964200-78966200	Enhancers	Fetal Kidney	kidney
21	chr15:78964200-78966400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:78964400-78965400	Enhancers	Brain Hippocampus Middle	brain
23	chr15:78964400-78965400	Enhancers	HMEC	breast
24	chr15:78964400-78965800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
25	chr15:78964400-78966000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr15:78964400-78966200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:78964400-78972800	Weak transcription	Fetal Brain Female	brain
28	chr15:78964600-78965400	Enhancers	Colon Smooth Muscle	Colon
29	chr15:78964800-78966000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:78965000-78965400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
31	chr15:78965000-78965800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
32	chr15:78965000-78968200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr15:78965000-78973200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:78965200-78965400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:78965200-78966000	Enhancers	Rectal Smooth Muscle	rectum

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