Variant report

Variant	rs12324748
Chromosome Location	chr15:40864636-40864637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10152546	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1044474	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10518697	0.93[EUR][1000 genomes]
rs1058734	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070283	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11630273	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11633184	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637245	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637422	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12385982	0.92[EUR][1000 genomes]
rs12441754	0.84[EUR][1000 genomes]
rs12903817	0.88[EUR][1000 genomes]
rs12907442	0.81[EUR][1000 genomes]
rs12908316	0.90[EUR][1000 genomes]
rs12913296	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12913739	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915171	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12915636	0.93[EUR][1000 genomes]
rs13329076	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17673703	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17674454	0.92[EUR][1000 genomes]
rs17747423	0.93[EUR][1000 genomes]
rs17747633	0.93[EUR][1000 genomes]
rs1814541	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1814542	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412525	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28529389	0.80[EUR][1000 genomes]
rs28634695	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28647196	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28669075	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34739056	0.83[EUR][1000 genomes]
rs34824658	0.89[EUR][1000 genomes]
rs35127391	0.93[EUR][1000 genomes]
rs35684277	0.87[EUR][1000 genomes]
rs35842610	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923880	0.91[EUR][1000 genomes]
rs4924486	0.91[EUR][1000 genomes]
rs62019876	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62019879	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71471880	0.87[EUR][1000 genomes]
rs7165509	0.87[EUR][1000 genomes]
rs7170288	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7175747	0.86[EUR][1000 genomes]
rs8029530	0.83[EUR][1000 genomes]
rs8036891	0.83[EUR][1000 genomes]
rs8037180	0.85[EUR][1000 genomes]
rs8038122	0.87[EUR][1000 genomes]
rs8042386	0.85[EUR][1000 genomes]
rs9920642	0.87[EUR][1000 genomes]
rs9920676	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription 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 target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12324748	RP11-111A22.1	cis	Artery Tibial	GTEx
rs12324748	C15orf57	cis	Artery Tibial	GTEx
rs12324748	C15orf57	cis	Heart Left Ventricle	GTEx
rs12324748	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs12324748	C15orf57	cis	Esophagus Mucosa	GTEx
rs12324748	RP11-111A22.1	cis	Artery Aorta	GTEx
rs12324748	C15orf57	cis	lung	GTEx
rs12324748	RP11-111A22.1	cis	lung	GTEx
rs12324748	C15orf57	cis	Artery Aorta	GTEx
rs12324748	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs12324748	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs12324748	C15orf57	cis	Nerve Tibial	GTEx
rs12324748	C15orf57	cis	Stomach	GTEx
rs12324748	C15orf57	cis	Muscle Skeletal	GTEx
rs12324748	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs12324748	C15orf57	cis	Esophagus Muscularis	GTEx
rs12324748	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs12324748	C15orf57	cis	Adipose Subcutaneous	GTEx
rs12324748	RP11-111A22.1	cis	Stomach	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40862400-40865600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:40862400-40865600	Weak transcription	Esophagus	oesophagus
3	chr15:40862600-40865600	Weak transcription	Left Ventricle	heart
4	chr15:40862800-40864800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:40862800-40867000	Strong transcription	Fetal Muscle Trunk	muscle
6	chr15:40862800-40875200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:40863000-40864800	Weak transcription	HSMMtube	muscle
8	chr15:40863000-40865000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:40863000-40865200	Weak transcription	Right Atrium	heart
10	chr15:40863000-40865400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:40863000-40865600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:40863000-40865600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:40863000-40865600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:40863000-40865600	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:40863000-40865600	Weak transcription	Psoas Muscle	Psoas
16	chr15:40863000-40865600	Weak transcription	A549	lung
17	chr15:40863000-40865600	Weak transcription	HSMM	muscle
18	chr15:40863000-40865800	Weak transcription	Colonic Mucosa	Colon
19	chr15:40863000-40865800	Weak transcription	Small Intestine	intestine
20	chr15:40863000-40868200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:40863000-40870200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr15:40863000-40875000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:40863000-40875000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:40863200-40864800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:40863200-40864800	Weak transcription	Brain Substantia Nigra	brain
26	chr15:40863200-40865400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:40863200-40865400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr15:40863200-40865400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr15:40863200-40865600	Weak transcription	NH-A	brain
30	chr15:40863200-40867200	Strong transcription	Fetal Muscle Leg	muscle
31	chr15:40863200-40868600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:40863200-40868800	Weak transcription	Fetal Heart	heart
33	chr15:40863200-40869000	Weak transcription	Fetal Brain Male	brain
34	chr15:40863600-40865200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:40863600-40866400	Strong transcription	Fetal Kidney	kidney
36	chr15:40863600-40866600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:40863600-40866800	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr15:40863600-40866800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:40863600-40867000	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr15:40863600-40867000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:40863600-40867000	Strong transcription	Osteobl	bone
42	chr15:40863600-40867200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:40863600-40867200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr15:40863600-40867200	Strong transcription	Primary B cells from cord blood	blood
45	chr15:40863600-40867200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:40863600-40867200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:40863600-40867200	Strong transcription	Brain Anterior Caudate	brain
48	chr15:40863600-40867400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:40863600-40867400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr15:40863600-40867400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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