Variant report

Variant	rs12441354
Chromosome Location	chr15:78821016-78821017
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	chr15:78818919..78821266-chr15:78825602..78827907,2	K562	blood:
2	chr15:78818397..78821568-chr15:78826002..78827936,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12438181	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12438659	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439240	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12441426	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2036534	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28395178	0.81[EUR][1000 genomes]
rs28437878	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28498264	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2869055	0.89[ASN][1000 genomes]
rs34138960	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34664138	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35212593	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3813570	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4461039	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs503464	0.83[EUR][1000 genomes]
rs57064725	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59133824	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59683676	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61204066	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs684513	0.82[EUR][1000 genomes]
rs7163730	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7169584	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173514	0.85[EUR][1000 genomes]
rs7181245	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7181447	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs905739	0.94[EUR][1000 genomes]
rs9788682	0.91[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12441354	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs12441354	IREB2	Cis_1M	lymphoblastoid	RTeQTL
rs12441354	CHRNA5	cis	Muscle Skeletal	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78800600-78822200	Weak transcription	Pancreas	Pancrea
2	chr15:78800600-78823600	Weak transcription	Gastric	stomach
3	chr15:78800800-78823400	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:78800800-78825600	Weak transcription	Brain Angular Gyrus	brain
5	chr15:78800800-78830800	Weak transcription	Right Ventricle	heart
6	chr15:78800800-78832000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr15:78800800-78832200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:78800800-78832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:78800800-78832400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:78801000-78825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:78801000-78829600	Weak transcription	Fetal Muscle Leg	muscle
12	chr15:78801000-78832200	Weak transcription	Adipose Nuclei	Adipose
13	chr15:78801000-78832200	Weak transcription	Fetal Kidney	kidney
14	chr15:78801000-78832200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:78801000-78832200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:78801000-78832200	Weak transcription	A549	lung
17	chr15:78803000-78832200	Weak transcription	Primary T cells from cord blood	blood
18	chr15:78810600-78832000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:78810600-78832400	Weak transcription	Aorta	Aorta
20	chr15:78810800-78832200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:78812000-78832200	Weak transcription	Fetal Stomach	stomach
22	chr15:78812400-78832200	Weak transcription	Fetal Intestine Large	intestine
23	chr15:78812600-78832200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr15:78816600-78832200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:78816800-78825400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:78817000-78832200	Weak transcription	Fetal Intestine Small	intestine
27	chr15:78820400-78821200	Strong transcription	Left Ventricle	heart
28	chr15:78820400-78821200	Strong transcription	Ovary	ovary
29	chr15:78820400-78821400	Strong transcription	Liver	Liver

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