Variant report

Variant	rs2290344
Chromosome Location	chr15:55619796-55619797
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	chr15:55618709..55621399-chr15:55623443..55625308,2	K562	blood:
2	chr15:55618646..55620160-chr15:55625270..55627647,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10851588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11071174	0.90[CHB][hapmap]
rs11071180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11071181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11490399	0.95[ASN][1000 genomes]
rs11629613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11630409	0.81[EUR][1000 genomes]
rs11632757	0.86[ASN][1000 genomes]
rs11635303	0.85[ASN][1000 genomes]
rs11635532	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11636687	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11638111	0.87[ASN][1000 genomes]
rs11638732	0.80[ASN][1000 genomes]
rs11639418	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs11639453	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11855382	0.87[ASN][1000 genomes]
rs11857303	0.92[ASN][1000 genomes]
rs12050587	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12050662	0.95[ASN][1000 genomes]
rs12050663	0.95[ASN][1000 genomes]
rs12050885	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs12050905	0.82[ASN][1000 genomes]
rs2290341	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2290343	0.97[ASN][1000 genomes]
rs2305424	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2414409	1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2444038	0.82[ASN][1000 genomes]
rs28540063	0.92[ASN][1000 genomes]
rs28636865	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28657774	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28668016	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28680176	0.95[ASN][1000 genomes]
rs28706887	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28748576	0.99[ASN][1000 genomes]
rs34848296	0.95[ASN][1000 genomes]
rs3743203	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4774760	0.91[ASN][1000 genomes]
rs4774764	0.94[ASN][1000 genomes]
rs4774766	0.86[CHB][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs55661134	0.95[ASN][1000 genomes]
rs55933611	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56159619	0.81[EUR][1000 genomes]
rs56257633	0.95[ASN][1000 genomes]
rs58701687	0.92[ASN][1000 genomes]
rs60338710	0.80[ASN][1000 genomes]
rs61573749	0.80[ASN][1000 genomes]
rs67230579	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67603645	0.88[ASN][1000 genomes]
rs692062	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs7162777	0.91[ASN][1000 genomes]
rs7174876	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7183157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7183960	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs72742273	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72742282	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8024695	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9920058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9920522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2290344	SLC27A2	cis	cerebellum	SCAN
rs2290344	PRTG	cis	cerebellum	SCAN
rs2290344	RAB27A	cis	parietal	SCAN
rs2290344	PIGB	cis	lymphoblastoid	seeQTL
rs2290344	RAB27A	cis	cerebellum	SCAN
rs2290344	PIGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55622400	Weak transcription	Left Ventricle	heart
2	chr15:55611800-55622400	Weak transcription	Lung	lung
3	chr15:55611800-55623200	Weak transcription	Spleen	Spleen
4	chr15:55611800-55623400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:55611800-55629600	Weak transcription	Pancreas	Pancrea
6	chr15:55611800-55640000	Weak transcription	Gastric	stomach
7	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
8	chr15:55612000-55620000	Weak transcription	Fetal Intestine Large	intestine
9	chr15:55612000-55622200	Weak transcription	Esophagus	oesophagus
10	chr15:55612000-55622200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:55612000-55622400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:55612000-55628400	Weak transcription	Fetal Brain Male	brain
13	chr15:55612000-55629800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:55612000-55630600	Weak transcription	Ovary	ovary
15	chr15:55612000-55635400	Weak transcription	Fetal Brain Female	brain
16	chr15:55612000-55636000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:55612000-55636000	Weak transcription	Brain Germinal Matrix	brain
18	chr15:55612000-55636400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:55612000-55665000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:55612000-55671000	Weak transcription	Right Ventricle	heart
21	chr15:55612000-55671000	Weak transcription	Small Intestine	intestine
22	chr15:55612400-55623000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:55612400-55623400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:55612400-55623400	Weak transcription	Fetal Muscle Leg	muscle
25	chr15:55612400-55625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:55612400-55627600	Weak transcription	Placenta	Placenta
27	chr15:55612400-55628200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:55612400-55631000	Weak transcription	HSMMtube	muscle
29	chr15:55612400-55635600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:55612600-55619800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:55612600-55620000	Weak transcription	Fetal Thymus	thymus
32	chr15:55612600-55620800	Weak transcription	Fetal Stomach	stomach
33	chr15:55612600-55622400	Weak transcription	Brain Anterior Caudate	brain
34	chr15:55612600-55622400	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:55612600-55622400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:55612600-55622800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:55612600-55623000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:55612600-55623000	Weak transcription	Thymus	Thymus
39	chr15:55612600-55623200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:55612600-55627200	Weak transcription	Fetal Lung	lung
41	chr15:55612600-55629600	Weak transcription	HSMM	muscle
42	chr15:55612600-55629800	Weak transcription	Brain Substantia Nigra	brain
43	chr15:55612600-55630000	Weak transcription	Brain Angular Gyrus	brain
44	chr15:55612600-55640400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:55612600-55650200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:55612600-55663600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:55612600-55675600	Weak transcription	Aorta	Aorta
48	chr15:55612800-55619800	Weak transcription	Adipose Nuclei	Adipose
49	chr15:55612800-55621800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:55612800-55622600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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