Variant report

Variant	rs1979908
Chromosome Location	chr15:78843564-78843565
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	chr15:78838010..78843726-chr15:78843842..78847469,5	MCF-7	breast:
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	chr15:78840813..78846169-chr15:78854868..78858995,9	MCF-7	breast:
6	chr15:78834823..78836611-chr15:78842594..78844710,2	MCF-7	breast:
7	chr15:78843179..78845391-chr15:78851308..78853669,4	K562	blood:
8	chr15:78730985..78732538-chr15:78840858..78843812,2	K562	blood:
9	chr15:78832914..78834536-chr15:78842167..78843719,2	MCF-7	breast:
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: 66 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11630349	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632604	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636131	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858230	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591557	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594391	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900612	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900783	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902493	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903129	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906284	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906846	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906951	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907169	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907425	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907966	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910100	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910289	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910726	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910969	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910978	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12912022	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12912673	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12913173	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12914694	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915366	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915428	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915652	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916483	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916999	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504545	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1504546	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407257	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1847530	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292117	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28392948	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28438420	0.89[EUR][1000 genomes]
rs2869055	0.88[EUR][1000 genomes]
rs2869544	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813571	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813572	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243083	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886571	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886572	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887062	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4887063	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887064	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5022780	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55690619	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56007453	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62008174	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62008193	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62008194	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7164030	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025429	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880395	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs905740	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952215	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952216	0.82[AMR][1000 genomes];0.94[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
rs1979908	CHRNA3	cis	Muscle Skeletal	GTEx
rs1979908	CHRNA5	cis	Heart Left Ventricle	GTEx
rs1979908	CHRNA5	cis	Muscle Skeletal	GTEx
rs1979908	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs1979908	RP11-650L12.2	cis	Esophagus Mucosa	GTEx
rs1979908	CHRNA5	cis	Nerve Tibial	GTEx
rs1979908	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs1979908	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs1979908	CHRNA5	cis	lung	GTEx
rs1979908	CHRNA5	cis	Esophagus Mucosa	GTEx
rs1979908	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs1979908	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs1979908	RP11-650L12.2	cis	lung	GTEx

Chromatin state (count:126 , 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	chr15:78834400-78843600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:78834400-78843600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:78834400-78843800	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:78834400-78843800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr15:78834600-78843600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:78834600-78843800	Strong transcription	Fetal Muscle Leg	muscle
8	chr15:78834800-78843600	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr15:78834800-78843600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:78834800-78843600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:78834800-78843600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr15:78834800-78843800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr15:78834800-78843800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:78834800-78843800	Strong transcription	Colon Smooth Muscle	Colon
15	chr15:78834800-78843800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr15:78834800-78844200	Strong transcription	Fetal Thymus	thymus
17	chr15:78835000-78843600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:78835000-78843600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:78835000-78843600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr15:78835000-78843600	Strong transcription	Fetal Intestine Large	intestine
21	chr15:78835000-78843600	Strong transcription	HSMM	muscle
22	chr15:78835000-78843800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:78835000-78843800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:78835000-78843800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:78835000-78843800	Strong transcription	Fetal Brain Female	brain
26	chr15:78835000-78844000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr15:78835000-78844000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:78835000-78844600	Strong transcription	Primary B cells from cord blood	blood
29	chr15:78835200-78843600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:78835200-78843600	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr15:78835200-78843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr15:78835400-78843800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:78835400-78843800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr15:78835600-78843600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:78835600-78843600	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:78835600-78843800	Strong transcription	Adipose Nuclei	Adipose
37	chr15:78835600-78843800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:78835600-78844000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:78835600-78844400	Strong transcription	Primary T cells from cord blood	blood
40	chr15:78835800-78843600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr15:78835800-78843600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:78835800-78843800	Strong transcription	Liver	Liver
43	chr15:78835800-78844200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:78835800-78844200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:78836200-78843600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:78836200-78857200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:78836800-78844000	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr15:78837000-78843800	Strong transcription	Brain Anterior Caudate	brain
49	chr15:78837000-78844200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr15:78837000-78844200	Strong transcription	Primary hematopoietic stem cells	blood

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