Variant report

Variant	rs7164594
Chromosome Location	chr15:78803057-78803058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12438181	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12438659	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12439240	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12441354	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12441426	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2036534	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28437878	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28498264	0.91[EUR][1000 genomes]
rs2869032	0.84[CEU][hapmap]
rs2869045	0.83[CEU][hapmap]
rs34138960	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34664138	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35212593	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3813570	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4461039	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4887053	0.83[CEU][hapmap]
rs503464	0.81[EUR][1000 genomes]
rs569207	0.82[CEU][hapmap]
rs57064725	0.84[EUR][1000 genomes]
rs59133824	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59683676	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61204066	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs667282	0.82[CEU][hapmap]
rs684513	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs7163730	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7169584	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7173514	0.83[EUR][1000 genomes]
rs7181245	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7181447	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs905739	0.92[EUR][1000 genomes]
rs9788682	0.94[CEU][hapmap];0.92[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
rs7164594	CHRNA5	cis	Muscle Skeletal	GTEx
rs7164594	IREB2	Cis_1M	lymphoblastoid	RTeQTL
rs7164594	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78800400-78812200	Weak transcription	Lung	lung
2	chr15:78800600-78813600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:78800600-78822200	Weak transcription	Pancreas	Pancrea
4	chr15:78800600-78823600	Weak transcription	Gastric	stomach
5	chr15:78800800-78806600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:78800800-78807400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:78800800-78807600	Weak transcription	Fetal Stomach	stomach
8	chr15:78800800-78810200	Weak transcription	Aorta	Aorta
9	chr15:78800800-78812000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:78800800-78813800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:78800800-78816400	Weak transcription	Ovary	ovary
12	chr15:78800800-78820800	Weak transcription	Psoas Muscle	Psoas
13	chr15:78800800-78823400	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:78800800-78825600	Weak transcription	Brain Angular Gyrus	brain
15	chr15:78800800-78830800	Weak transcription	Right Ventricle	heart
16	chr15:78800800-78832000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:78800800-78832200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:78800800-78832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:78800800-78832400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:78801000-78805600	Weak transcription	Left Ventricle	heart
21	chr15:78801000-78809600	Weak transcription	Liver	Liver
22	chr15:78801000-78810000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr15:78801000-78810400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:78801000-78812800	Weak transcription	Brain Anterior Caudate	brain
25	chr15:78801000-78813400	Weak transcription	Brain Hippocampus Middle	brain
26	chr15:78801000-78813600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:78801000-78817800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:78801000-78818200	Weak transcription	Colonic Mucosa	Colon
29	chr15:78801000-78825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:78801000-78829600	Weak transcription	Fetal Muscle Leg	muscle
31	chr15:78801000-78832200	Weak transcription	Adipose Nuclei	Adipose
32	chr15:78801000-78832200	Weak transcription	Fetal Kidney	kidney
33	chr15:78801000-78832200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr15:78801000-78832200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:78801000-78832200	Weak transcription	A549	lung
36	chr15:78801200-78806800	Weak transcription	Fetal Intestine Large	intestine
37	chr15:78801400-78806800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:78801400-78810200	Weak transcription	Fetal Intestine Small	intestine
39	chr15:78801800-78806800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:78802400-78815800	Weak transcription	HepG2	liver
41	chr15:78802600-78813600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:78802600-78813800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr15:78802800-78813200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:78803000-78832200	Weak transcription	Primary T cells from cord blood	blood

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