Variant report

Variant	rs905740
Chromosome Location	chr15:78844386-78844387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:78844003..78845527-chr15:78845642..78848545,2	K562	blood:
2	chr15:78831431..78836974-chr15:78839813..78847662,20	MCF-7	breast:
3	chr15:78843495..78845892-chr15:78851600..78855221,3	K562	blood:
4	chr15:78841640..78845240-chr15:78856140..78858559,3	K562	blood:
5	chr15:78838010..78843726-chr15:78843842..78847469,5	MCF-7	breast:
6	chr15:78840813..78846169-chr15:78854868..78858995,9	MCF-7	breast:
7	chr15:78844056..78846099-chr15:78848008..78850321,3	K562	blood:
8	chr15:78834823..78836611-chr15:78842594..78844710,2	MCF-7	breast:
9	chr15:78843179..78845391-chr15:78851308..78853669,4	K562	blood:
10	chr15:78843350..78846204-chr15:78880835..78882358,2	K562	blood:
11	chr15:78799588..78802030-chr15:78842026..78844703,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000169684	Chromatin interaction
ENSG00000188266	Chromatin interaction
ENSG00000041357	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11630349	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632604	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636131	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858230	0.95[CEU][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591557	0.96[CEU][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594391	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900612	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900783	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902493	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903129	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906284	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906846	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906951	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907169	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907425	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907966	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910100	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910289	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910726	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910969	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910978	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12912022	0.89[EUR][1000 genomes]
rs12912673	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12913173	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12914694	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915366	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915428	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915652	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916483	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916999	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504545	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1504546	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504548	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407257	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1847530	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979905	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979906	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979907	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979908	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292117	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28392948	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28438420	0.88[EUR][1000 genomes]
rs2869055	0.87[EUR][1000 genomes]
rs2869544	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813571	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813572	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243083	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4275821	0.84[CEU][hapmap];0.89[YRI][hapmap]
rs481134	0.84[CEU][hapmap]
rs4886571	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886572	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887062	0.96[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4887063	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887064	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5022780	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs555018	0.84[CEU][hapmap]
rs55690619	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56007453	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588765	0.87[CEU][hapmap]
rs601079	0.85[CEU][hapmap]
rs62008174	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62008193	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62008194	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs621849	0.84[CEU][hapmap]
rs647041	0.80[CEU][hapmap]
rs6495306	0.84[CEU][hapmap]
rs6495307	0.81[CEU][hapmap]
rs680244	0.84[CEU][hapmap]
rs7164030	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173512	0.84[CEU][hapmap];0.89[YRI][hapmap]
rs8025429	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880395	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs952215	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952216	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs905740	CHRNA5	cis	lung	GTEx
rs905740	CHRNA5	cis	Heart Left Ventricle	GTEx
rs905740	CHRNA5	cis	Muscle Skeletal	GTEx
rs905740	CHRNA5	cis	Esophagus Mucosa	GTEx
rs905740	CHRNA5	cis	Nerve Tibial	GTEx
rs905740	CHRNA3	cis	Muscle Skeletal	GTEx
rs905740	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs905740	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs905740	RP11-650L12.2	cis	Esophagus Mucosa	GTEx
rs905740	RP11-650L12.2	cis	lung	GTEx
rs905740	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs905740	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs905740	CHRNA5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78834200-78845000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:78835000-78844600	Strong transcription	Primary B cells from cord blood	blood
3	chr15:78835600-78844400	Strong transcription	Primary T cells from cord blood	blood
4	chr15:78836200-78857200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:78837800-78844600	Strong transcription	Left Ventricle	heart
6	chr15:78839800-78844600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:78841200-78856800	Weak transcription	Hela-S3	cervix
8	chr15:78841800-78844800	Weak transcription	HSMMtube	muscle
9	chr15:78842000-78844400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:78842000-78845000	Weak transcription	Ovary	ovary
11	chr15:78842000-78845800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:78842000-78857400	Weak transcription	Psoas Muscle	Psoas
13	chr15:78842200-78845200	Weak transcription	Fetal Kidney	kidney
14	chr15:78842200-78848600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:78842400-78844600	Weak transcription	Fetal Brain Male	brain
16	chr15:78842400-78845000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:78842400-78845400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:78842400-78845600	Weak transcription	Osteobl	bone
19	chr15:78842400-78846400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr15:78842600-78844600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr15:78842600-78845000	Weak transcription	NHDF-Ad	bronchial
22	chr15:78842600-78845200	Weak transcription	Colonic Mucosa	Colon
23	chr15:78842800-78845000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:78843000-78845000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:78843000-78845000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:78843000-78845400	Weak transcription	NHEK	skin
27	chr15:78843000-78845800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:78843000-78845800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:78843000-78845800	Weak transcription	Brain Angular Gyrus	brain
30	chr15:78843000-78846000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:78843000-78846600	Weak transcription	NHLF	lung
32	chr15:78843000-78848600	Weak transcription	Brain Substantia Nigra	brain
33	chr15:78843000-78857200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr15:78843200-78844600	Weak transcription	HUVEC	blood vessel
35	chr15:78843200-78845000	Weak transcription	Pancreas	Pancrea
36	chr15:78843200-78845200	Weak transcription	NH-A	brain
37	chr15:78843200-78845400	Weak transcription	Fetal Intestine Small	intestine
38	chr15:78843200-78846200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr15:78843200-78846400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:78843200-78857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:78843400-78844600	Weak transcription	Small Intestine	intestine
42	chr15:78843400-78845200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:78843400-78845400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:78843400-78845600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:78843400-78845600	Weak transcription	Lung	lung
46	chr15:78843400-78845800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:78843400-78846400	Weak transcription	Placenta	Placenta
48	chr15:78843400-78846400	Weak transcription	HMEC	breast
49	chr15:78843400-78847000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:78843400-78847000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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