Variant report

Variant	rs922691
Chromosome Location	chr15:78963994-78963995
allele	C/T
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: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11637890	1.00[JPT][hapmap]
rs12901241	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12905641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915539	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28444683	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34275594	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34694149	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35704045	0.82[EUR][1000 genomes]
rs58946838	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61630816	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7169223	0.83[EUR][1000 genomes]
rs7178007	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181405	0.96[CEU][hapmap];0.82[GIH][hapmap]
rs8038920	0.87[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs922691	CHRNA5	cis	Muscle Skeletal	GTEx
rs922691	IREB2	cis	cerebellum	SCAN
rs922691	FAH	cis	parietal	SCAN
rs922691	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs922691	CHRNA5	cis	cerebellum	SCAN
rs922691	CHRNA5	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78957000-78964200	Weak transcription	Fetal Kidney	kidney
2	chr15:78960600-78964200	Weak transcription	Left Ventricle	heart
3	chr15:78960600-78964200	Weak transcription	Right Ventricle	heart
4	chr15:78960800-78964200	Weak transcription	HepG2	liver
5	chr15:78961000-78964000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:78961600-78964800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:78961800-78964200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:78962000-78964000	Weak transcription	Fetal Stomach	stomach
9	chr15:78963600-78964200	Weak transcription	Fetal Brain Male	brain
10	chr15:78963600-78964600	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr15:78963600-78964800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr15:78963600-78965000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr15:78963600-78965000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr15:78963600-78965000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr15:78963600-78965200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:78963600-78965400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:78963600-78965600	Enhancers	Fetal Lung	lung
18	chr15:78963600-78966000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
19	chr15:78963600-78966200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:78963600-78966600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr15:78963800-78964000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr15:78963800-78964200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr15:78963800-78964400	Enhancers	Brain Germinal Matrix	brain
24	chr15:78963800-78965200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr15:78963800-78965400	Enhancers	Esophagus	oesophagus
26	chr15:78963800-78966000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr15:78963800-78966000	Enhancers	Adipose Nuclei	Adipose
28	chr15:78963800-78966000	Enhancers	Fetal Muscle Leg	muscle
29	chr15:78963800-78966400	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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