Variant report

Variant	rs9788682
Chromosome Location	chr15:78802586-78802587
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	chr15:78797464..78804546-chr15:78829529..78835433,12	MCF-7	breast:
2	chr15:78798632..78801641-chr15:78802047..78805742,4	K562	blood:

Variant related genes	Relation type
ENSG00000041357	Chromatin interaction
ENSG00000268838	Chromatin interaction
ENSG00000188266	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11072766	0.82[CEU][hapmap]
rs12438181	0.92[EUR][1000 genomes]
rs12438659	0.91[EUR][1000 genomes]
rs12439240	0.87[EUR][1000 genomes]
rs12441354	0.91[EUR][1000 genomes]
rs12441426	0.93[EUR][1000 genomes]
rs2036534	0.94[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2568483	0.82[CEU][hapmap]
rs2568485	0.81[CEU][hapmap]
rs2568488	0.82[CEU][hapmap]
rs2656069	0.82[CEU][hapmap]
rs2656071	0.82[CEU][hapmap]
rs2656073	0.82[CEU][hapmap]
rs28395178	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28437878	0.93[EUR][1000 genomes]
rs28498264	0.87[EUR][1000 genomes]
rs2869032	0.88[CEU][hapmap]
rs2869045	0.88[CEU][hapmap]
rs2938674	0.82[CEU][hapmap]
rs34138960	0.88[EUR][1000 genomes]
rs34664138	0.88[EUR][1000 genomes]
rs35212593	0.88[EUR][1000 genomes]
rs3813570	0.94[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs4461039	0.94[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs4887053	0.88[CEU][hapmap]
rs59133824	0.88[EUR][1000 genomes]
rs59683676	0.88[EUR][1000 genomes]
rs61204066	0.92[EUR][1000 genomes]
rs684513	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7163730	0.94[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs7164594	0.94[CEU][hapmap]
rs7169584	0.91[EUR][1000 genomes]
rs7181245	0.91[EUR][1000 genomes]
rs7181447	0.91[EUR][1000 genomes]
rs905739	0.88[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9788682	IREB2	Cis_1M	lymphoblastoid	RTeQTL
rs9788682	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs9788682	PSMA4	cis	cerebellum	SCAN
rs9788682	LOXL1	cis	cerebellum	SCAN
rs9788682	COX5A	cis	parietal	SCAN
rs9788682	PSMA4	cis	parietal	SCAN
rs9788682	CHRNA5	cis	cerebellum	SCAN
rs9788682	CHRNA5	cis	parietal	SCAN
rs9788682	CHRNA5	cis	Muscle Skeletal	GTEx

Chromatin state (count:47 , 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	chr15:78800800-78802600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr15:78800800-78802800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr15:78800800-78806600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:78800800-78807400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:78800800-78807600	Weak transcription	Fetal Stomach	stomach
10	chr15:78800800-78810200	Weak transcription	Aorta	Aorta
11	chr15:78800800-78812000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:78800800-78813800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:78800800-78816400	Weak transcription	Ovary	ovary
14	chr15:78800800-78820800	Weak transcription	Psoas Muscle	Psoas
15	chr15:78800800-78823400	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:78800800-78825600	Weak transcription	Brain Angular Gyrus	brain
17	chr15:78800800-78830800	Weak transcription	Right Ventricle	heart
18	chr15:78800800-78832000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:78800800-78832200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:78800800-78832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:78800800-78832400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:78801000-78805600	Weak transcription	Left Ventricle	heart
23	chr15:78801000-78809600	Weak transcription	Liver	Liver
24	chr15:78801000-78810000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:78801000-78810400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:78801000-78812800	Weak transcription	Brain Anterior Caudate	brain
27	chr15:78801000-78813400	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:78801000-78813600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr15:78801000-78817800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:78801000-78818200	Weak transcription	Colonic Mucosa	Colon
31	chr15:78801000-78825600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:78801000-78829600	Weak transcription	Fetal Muscle Leg	muscle
33	chr15:78801000-78832200	Weak transcription	Adipose Nuclei	Adipose
34	chr15:78801000-78832200	Weak transcription	Fetal Kidney	kidney
35	chr15:78801000-78832200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:78801000-78832200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:78801000-78832200	Weak transcription	A549	lung
38	chr15:78801200-78806800	Weak transcription	Fetal Intestine Large	intestine
39	chr15:78801400-78802600	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr15:78801400-78806800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr15:78801400-78810200	Weak transcription	Fetal Intestine Small	intestine
42	chr15:78801800-78802600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr15:78801800-78803000	Enhancers	Primary T cells from cord blood	blood
44	chr15:78801800-78806800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:78802000-78802600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr15:78802200-78802600	Enhancers	Primary T cells fromperipheralblood	blood
47	chr15:78802400-78815800	Weak transcription	HepG2	liver

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