Variant report

Variant	rs8053
Chromosome Location	chr15:78841220-78841221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr15:78809980..78812822-chr15:78838662..78841317,2	K562	blood:
4	chr15:78841072..78843191-chr15:78856342..78859317,3	K562	blood:
5	chr15:78840813..78846169-chr15:78854868..78858995,9	MCF-7	breast:
6	chr15:78730985..78732538-chr15:78840858..78843812,2	K562	blood:

Variant related genes	Relation type
ENSG00000041357	Chromatin interaction
ENSG00000169684	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11630349	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591557	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594391	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900612	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900783	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903129	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906284	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906846	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907169	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907425	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910100	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910726	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910969	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910978	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12912022	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12912673	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12913173	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12914694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915366	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915428	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915652	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1504546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504548	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17407257	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1847530	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979906	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979908	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292117	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28392948	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28438420	0.91[EUR][1000 genomes]
rs2869055	0.89[EUR][1000 genomes]
rs2869544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3743077	0.83[TSI][hapmap]
rs3813571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4275821	0.87[CEU][hapmap];0.94[YRI][hapmap]
rs472054	0.80[GIH][hapmap]
rs481134	0.84[CEU][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap]
rs4886571	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886572	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887062	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4887063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4887064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5022780	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs555018	0.83[CEU][hapmap]
rs55690619	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56007453	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs588765	0.86[CEU][hapmap]
rs601079	0.84[CEU][hapmap]
rs615470	0.80[GIH][hapmap]
rs62008174	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62008193	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62008194	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs621849	0.84[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs6495306	0.84[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs660652	0.80[GIH][hapmap]
rs680244	0.84[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap]
rs7164030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173512	0.87[CEU][hapmap];0.94[YRI][hapmap]
rs8025429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs905740	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]
rs952215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs8053	CHRNA5	cis	cerebellum	SCAN
rs8053	CHRNA5	cis	Heart Left Ventricle	GTEx
rs8053	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs8053	CHRNA5	cis	Muscle Skeletal	GTEx
rs8053	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs8053	CHRNA5	cis	Nerve Tibial	GTEx
rs8053	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs8053	IREB2	cis	parietal	SCAN
rs8053	CHRNA3	cis	Muscle Skeletal	GTEx
rs8053	CHRNA5	cis	parietal	SCAN
rs8053	CHRNA5	cis	Esophagus Mucosa	GTEx
rs8053	RP11-650L12.2	cis	lung	GTEx
rs8053	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs8053	RP11-650L12.2	cis	Esophagus Mucosa	GTEx
rs8053	CHRNA5	cis	lung	GTEx
rs8053	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs8053	IREB2	cis	cerebellum	SCAN
rs8053	PSMA4	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78834200-78843400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
2	chr15:78834200-78843400	Strong transcription	Placenta	Placenta
3	chr15:78834200-78845000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:78834400-78843600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:78834400-78843600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:78834400-78843800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:78834400-78843800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr15:78834600-78843200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:78834600-78843600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:78834600-78843800	Strong transcription	Fetal Muscle Leg	muscle
11	chr15:78834800-78842400	Strong transcription	Osteobl	bone
12	chr15:78834800-78843200	Strong transcription	HUVEC	blood vessel
13	chr15:78834800-78843400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:78834800-78843600	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr15:78834800-78843600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:78834800-78843600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:78834800-78843600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr15:78834800-78843800	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr15:78834800-78843800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:78834800-78843800	Strong transcription	Colon Smooth Muscle	Colon
21	chr15:78834800-78843800	Strong transcription	Stomach Smooth Muscle	stomach
22	chr15:78834800-78844200	Strong transcription	Fetal Thymus	thymus
23	chr15:78835000-78842200	Strong transcription	HMEC	breast
24	chr15:78835000-78842800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:78835000-78843600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:78835000-78843600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:78835000-78843600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr15:78835000-78843600	Strong transcription	Fetal Intestine Large	intestine
29	chr15:78835000-78843600	Strong transcription	HSMM	muscle
30	chr15:78835000-78843800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:78835000-78843800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:78835000-78843800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:78835000-78843800	Strong transcription	Fetal Brain Female	brain
34	chr15:78835000-78844000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr15:78835000-78844000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:78835000-78844600	Strong transcription	Primary B cells from cord blood	blood
37	chr15:78835200-78843600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:78835200-78843600	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr15:78835200-78843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr15:78835400-78843800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:78835400-78843800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr15:78835600-78843000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:78835600-78843600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:78835600-78843600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:78835600-78843800	Strong transcription	Adipose Nuclei	Adipose
46	chr15:78835600-78843800	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:78835600-78844000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:78835600-78844400	Strong transcription	Primary T cells from cord blood	blood
49	chr15:78835800-78843400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:78835800-78843400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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