Variant report

Variant	rs7182499
Chromosome Location	chr15:41020610-41020611
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	chr15:40992580..40995462-chr15:41019256..41021826,2	K562	blood:

Variant related genes	Relation type
ENSG00000051180	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10518697	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11070283	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12148915	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12385982	0.82[AMR][1000 genomes]
rs12442560	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591044	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592524	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903817	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12907442	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12908316	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12915636	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17674454	0.82[AMR][1000 genomes]
rs17747423	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17747633	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1801321	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2619682	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28529389	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28866515	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28891195	0.82[AMR][1000 genomes]
rs34305357	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34739056	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35127391	0.84[AMR][1000 genomes]
rs35684277	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4923880	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4924486	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4924492	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924496	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924498	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924502	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5030789	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56409425	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59244061	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492964	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71471880	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7165509	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7175747	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7175905	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7176245	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176590	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7177265	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180135	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029530	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8036891	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8037180	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8038122	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8042386	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs957603	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920676	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7182499	C15orf57	cis	Nerve Tibial	GTEx
rs7182499	RP11-111A22.1	cis	lung	GTEx
rs7182499	RP11-111A22.1	cis	Artery Tibial	GTEx
rs7182499	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs7182499	C15orf57	cis	Muscle Skeletal	GTEx
rs7182499	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs7182499	C15orf57	cis	Artery Aorta	GTEx
rs7182499	C15orf57	cis	Esophagus Muscularis	GTEx
rs7182499	C15orf57	cis	Esophagus Mucosa	GTEx
rs7182499	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs7182499	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs7182499	C15orf57	cis	lung	GTEx
rs7182499	C15orf57	cis	Adipose Subcutaneous	GTEx
rs7182499	C15orf57	cis	Artery Tibial	GTEx
rs7182499	C15orf57	cis	Heart Left Ventricle	GTEx
rs7182499	C15orf57	cis	Stomach	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
2	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
3	chr15:40988400-41020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr15:40988400-41021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr15:40988400-41021800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
7	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:40988600-41021400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:40988600-41021400	Weak transcription	Fetal Brain Female	brain
10	chr15:40988800-41021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:40988800-41021800	Weak transcription	Fetal Kidney	kidney
12	chr15:40990600-41022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:40993200-41025800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:40997800-41020800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:40998200-41023200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
17	chr15:40999000-41027600	Weak transcription	Gastric	stomach
18	chr15:40999200-41021600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:41000000-41026000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:41001400-41020800	Weak transcription	NHDF-Ad	bronchial
21	chr15:41002000-41021400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:41002200-41021600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:41003200-41021800	Weak transcription	Brain Germinal Matrix	brain
24	chr15:41003600-41021800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:41003800-41023800	Weak transcription	Fetal Lung	lung
26	chr15:41004000-41021600	Weak transcription	Osteobl	bone
27	chr15:41004600-41021000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:41004800-41022000	Weak transcription	A549	lung
29	chr15:41004800-41023400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:41005000-41021400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:41006400-41021800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:41007400-41020800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr15:41008200-41046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr15:41010400-41021800	Weak transcription	HSMMtube	muscle
35	chr15:41010800-41021600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:41011200-41020800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:41011200-41021400	Weak transcription	Thymus	Thymus
38	chr15:41011200-41021600	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:41011200-41021800	Weak transcription	GM12878-XiMat	blood
40	chr15:41011400-41021600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:41012800-41021600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:41012800-41021600	Weak transcription	Fetal Intestine Large	intestine
43	chr15:41012800-41023600	Weak transcription	Brain Substantia Nigra	brain
44	chr15:41012800-41028200	Weak transcription	NHLF	lung
45	chr15:41013200-41020800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:41013200-41020800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:41013200-41021000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:41013400-41020800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:41014200-41021600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:41014200-41022200	Weak transcription	HUVEC	blood vessel

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