Variant report

Variant	rs12905641
Chromosome Location	chr15:78964362-78964363
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: 25 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs11637890	1.00[JPT][hapmap]
rs12324870	0.82[EUR][1000 genomes]
rs12901241	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12905273	0.81[EUR][1000 genomes]
rs12910237	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12915539	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28444683	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34275594	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34694149	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35704045	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58946838	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61630816	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7169223	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7178007	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181405	0.92[CEU][hapmap];0.82[GIH][hapmap]
rs8038920	0.91[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs922691	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12905641	UBL7	cis	parietal	SCAN
rs12905641	CHRNA3	cis	Muscle Skeletal	GTEx
rs12905641	CHRNA5	cis	multi-tissue	Pritchard
rs12905641	IREB2	cis	cerebellum	SCAN
rs12905641	CHRNA5	cis	parietal	SCAN
rs12905641	FAH	cis	parietal	SCAN
rs12905641	TMED3	cis	parietal	SCAN
rs12905641	CHRNA5	cis	Muscle Skeletal	GTEx
rs12905641	CHRNA5	cis	cerebellum	SCAN
rs12905641	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78961600-78964800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:78963600-78964600	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr15:78963600-78964800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr15:78963600-78965000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr15:78963600-78965000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr15:78963600-78965000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr15:78963600-78965200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:78963600-78965400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:78963600-78965600	Enhancers	Fetal Lung	lung
10	chr15:78963600-78966000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr15:78963600-78966200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:78963600-78966600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr15:78963800-78964400	Enhancers	Brain Germinal Matrix	brain
14	chr15:78963800-78965200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr15:78963800-78965400	Enhancers	Esophagus	oesophagus
16	chr15:78963800-78966000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr15:78963800-78966000	Enhancers	Adipose Nuclei	Adipose
18	chr15:78963800-78966000	Enhancers	Fetal Muscle Leg	muscle
19	chr15:78963800-78966400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr15:78964000-78964400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr15:78964000-78964400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:78964000-78964400	Enhancers	Fetal Brain Female	brain
23	chr15:78964000-78964400	Enhancers	Placenta	Placenta
24	chr15:78964000-78965000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:78964000-78965000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:78964000-78965000	Enhancers	Psoas Muscle	Psoas
27	chr15:78964000-78965400	Enhancers	Fetal Stomach	stomach
28	chr15:78964000-78966600	Enhancers	Spleen	Spleen
29	chr15:78964000-78966800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr15:78964200-78964600	Enhancers	Gastric	stomach
31	chr15:78964200-78964600	Enhancers	Left Ventricle	heart
32	chr15:78964200-78964600	Enhancers	Right Ventricle	heart
33	chr15:78964200-78965200	Enhancers	Fetal Brain Male	brain
34	chr15:78964200-78965400	Enhancers	HepG2	liver
35	chr15:78964200-78965600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:78964200-78965600	Enhancers	Brain Anterior Caudate	brain
37	chr15:78964200-78965600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr15:78964200-78965600	Enhancers	HSMMtube	muscle
39	chr15:78964200-78966000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr15:78964200-78966200	Enhancers	Fetal Kidney	kidney
41	chr15:78964200-78966400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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