Variant report

Variant	rs12910100
Chromosome Location	chr15:78822667-78822668
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	chr15:78815420..78817422-chr15:78821407..78822999,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs11630349	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632604	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636131	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858230	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12591557	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12594391	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900612	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900783	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12902493	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903129	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906284	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906846	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906951	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907169	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907425	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907966	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910289	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910726	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910969	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12910978	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12912022	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912673	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12913173	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12914694	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915366	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915428	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915652	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12916483	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916999	0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504545	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1504546	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1504548	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17407257	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1847530	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979905	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979906	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979907	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1979908	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292117	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28392948	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28438420	0.91[EUR][1000 genomes]
rs2869055	0.93[EUR][1000 genomes]
rs2869544	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813571	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813572	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243083	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886571	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886572	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4887062	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4887063	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4887064	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5022780	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55690619	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56007453	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62008174	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62008193	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62008194	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7164030	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8025429	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8053	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs880395	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs905740	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs952215	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952216	0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12910100	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs12910100	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs12910100	CHRNA5	cis	Heart Left Ventricle	GTEx
rs12910100	RP11-650L12.2	cis	lung	GTEx
rs12910100	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs12910100	CHRNA3	cis	Muscle Skeletal	GTEx
rs12910100	CHRNA5	cis	lung	GTEx
rs12910100	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs12910100	CHRNA5	cis	Nerve Tibial	GTEx
rs12910100	CHRNA5	cis	Esophagus Mucosa	GTEx
rs12910100	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs12910100	CHRNA5	cis	Muscle Skeletal	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78800600-78823600	Weak transcription	Gastric	stomach
2	chr15:78800800-78823400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:78800800-78825600	Weak transcription	Brain Angular Gyrus	brain
4	chr15:78800800-78830800	Weak transcription	Right Ventricle	heart
5	chr15:78800800-78832000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:78800800-78832200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:78800800-78832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:78800800-78832400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:78801000-78825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:78801000-78829600	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:78801000-78832200	Weak transcription	Adipose Nuclei	Adipose
12	chr15:78801000-78832200	Weak transcription	Fetal Kidney	kidney
13	chr15:78801000-78832200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:78801000-78832200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:78801000-78832200	Weak transcription	A549	lung
16	chr15:78803000-78832200	Weak transcription	Primary T cells from cord blood	blood
17	chr15:78810600-78832000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:78810600-78832400	Weak transcription	Aorta	Aorta
19	chr15:78810800-78832200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:78812000-78832200	Weak transcription	Fetal Stomach	stomach
21	chr15:78812400-78832200	Weak transcription	Fetal Intestine Large	intestine
22	chr15:78812600-78832200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:78816600-78832200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:78816800-78825400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:78817000-78832200	Weak transcription	Fetal Intestine Small	intestine
26	chr15:78821200-78832200	Weak transcription	Left Ventricle	heart
27	chr15:78821200-78832400	Weak transcription	Ovary	ovary
28	chr15:78821400-78832200	Weak transcription	Liver	Liver

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