Variant report

Variant	rs62008193
Chromosome Location	chr15:78813334-78813335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78811936..78813668-chr15:78822853..78825846,2	MCF-7	breast:
2	chr15:78802902..78805287-chr15:78811906..78814563,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs11630349	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11632604	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11636131	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11858230	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591557	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12594391	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12900612	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12900783	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12902493	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12903129	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12906284	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12906846	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12906951	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12907169	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12907425	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907966	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910100	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910289	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910726	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12910969	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12910978	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12912022	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12912673	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12913173	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12914694	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12915366	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12915428	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12915652	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12916483	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916999	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1504545	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1504546	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1504548	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17407257	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1847530	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1979905	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1979906	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1979907	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1979908	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2292117	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28392948	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28438420	0.84[EUR][1000 genomes]
rs2869055	0.85[EUR][1000 genomes]
rs2869544	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3813571	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3813572	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4243083	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886571	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886572	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4887062	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4887063	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4887064	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5022780	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55690619	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56007453	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62008174	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62008194	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7164030	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8025429	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8053	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs880395	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs905740	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs952215	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs952216	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs62008193	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs62008193	CHRNA5	cis	Heart Left Ventricle	GTEx
rs62008193	RP11-650L12.2	cis	lung	GTEx
rs62008193	CHRNA5	cis	Muscle Skeletal	GTEx
rs62008193	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs62008193	CHRNA5	cis	Nerve Tibial	GTEx
rs62008193	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs62008193	CHRNA5	cis	lung	GTEx
rs62008193	CHRNA3	cis	Muscle Skeletal	GTEx
rs62008193	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs62008193	CHRNA5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78800600-78813600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr15:78800600-78822200	Weak transcription	Pancreas	Pancrea
3	chr15:78800600-78823600	Weak transcription	Gastric	stomach
4	chr15:78800800-78813800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:78800800-78816400	Weak transcription	Ovary	ovary
6	chr15:78800800-78820800	Weak transcription	Psoas Muscle	Psoas
7	chr15:78800800-78823400	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:78800800-78825600	Weak transcription	Brain Angular Gyrus	brain
9	chr15:78800800-78830800	Weak transcription	Right Ventricle	heart
10	chr15:78800800-78832000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:78800800-78832200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:78800800-78832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:78800800-78832400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:78801000-78813400	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:78801000-78813600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr15:78801000-78817800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:78801000-78818200	Weak transcription	Colonic Mucosa	Colon
18	chr15:78801000-78825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:78801000-78829600	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:78801000-78832200	Weak transcription	Adipose Nuclei	Adipose
21	chr15:78801000-78832200	Weak transcription	Fetal Kidney	kidney
22	chr15:78801000-78832200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:78801000-78832200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:78801000-78832200	Weak transcription	A549	lung
25	chr15:78802400-78815800	Weak transcription	HepG2	liver
26	chr15:78802600-78813600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr15:78802600-78813800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr15:78803000-78832200	Weak transcription	Primary T cells from cord blood	blood
29	chr15:78810400-78818200	Weak transcription	Liver	Liver
30	chr15:78810600-78832000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:78810600-78832400	Weak transcription	Aorta	Aorta
32	chr15:78810800-78832200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:78812000-78832200	Weak transcription	Fetal Stomach	stomach
34	chr15:78812200-78816200	Weak transcription	Fetal Intestine Small	intestine
35	chr15:78812200-78820400	Weak transcription	Left Ventricle	heart
36	chr15:78812400-78832200	Weak transcription	Fetal Intestine Large	intestine
37	chr15:78812600-78815400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:78812600-78816200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:78812600-78832200	Weak transcription	Stomach Smooth Muscle	stomach

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