Variant report

Variant	rs28647196
Chromosome Location	chr15:40833379-40833380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40825965..40829345-chr15:40829678..40833688,6	K562	blood:
2	chr15:40825263..40828833-chr15:40829678..40833530,4	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10152546	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1044474	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518697	0.82[EUR][1000 genomes]
rs1058734	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070283	0.82[EUR][1000 genomes]
rs11630273	0.84[EUR][1000 genomes]
rs11633184	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637245	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637422	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12324748	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12385982	0.82[EUR][1000 genomes]
rs12913296	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913739	0.84[EUR][1000 genomes]
rs12915171	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12915636	0.83[EUR][1000 genomes]
rs13329076	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17673703	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17674454	0.82[EUR][1000 genomes]
rs17747423	0.82[EUR][1000 genomes]
rs17747633	0.82[EUR][1000 genomes]
rs1814541	0.84[EUR][1000 genomes]
rs2412525	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28634695	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669075	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35127391	0.84[EUR][1000 genomes]
rs35842610	0.84[EUR][1000 genomes]
rs4923880	0.81[EUR][1000 genomes]
rs4924486	0.80[EUR][1000 genomes]
rs62019876	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62019879	0.84[EUR][1000 genomes]
rs7170288	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9920676	0.82[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs28647196	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs28647196	C15orf57	cis	Stomach	GTEx
rs28647196	CCDC32	cis	multi-tissue	Pritchard
rs28647196	C15orf57	cis	lung	GTEx
rs28647196	RAD51	cis	multi-tissue	Pritchard
rs28647196	C15orf57	cis	Adipose Subcutaneous	GTEx
rs28647196	C15orf57	cis	Artery Tibial	GTEx
rs28647196	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs28647196	RP11-111A22.1	cis	lung	GTEx
rs28647196	C15orf57	cis	Esophagus Muscularis	GTEx
rs28647196	C15orf57	cis	Muscle Skeletal	GTEx
rs28647196	C15orf57	cis	Nerve Tibial	GTEx
rs28647196	RP11-111A22.1	cis	Artery Tibial	GTEx
rs28647196	C15orf57	cis	Heart Left Ventricle	GTEx
rs28647196	C15orf57	cis	Artery Aorta	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40812400-40837800	Weak transcription	Lung	lung
2	chr15:40812600-40840600	Weak transcription	Hela-S3	cervix
3	chr15:40816800-40835000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:40816800-40845600	Weak transcription	Ovary	ovary
5	chr15:40819600-40845000	Weak transcription	Pancreas	Pancrea
6	chr15:40820800-40833800	Weak transcription	K562	blood
7	chr15:40821400-40836800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:40821400-40848000	Weak transcription	Brain Anterior Caudate	brain
9	chr15:40821800-40840400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:40821800-40856400	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:40822600-40856400	Weak transcription	Small Intestine	intestine
12	chr15:40823200-40839600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:40823800-40841800	Weak transcription	Brain Substantia Nigra	brain
14	chr15:40824800-40842600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:40825000-40836200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:40825600-40839400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:40825600-40840000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr15:40825800-40839200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:40825800-40839600	Weak transcription	NHEK	skin
20	chr15:40827600-40842000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:40827800-40835400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:40827800-40839200	Weak transcription	Fetal Thymus	thymus
23	chr15:40828000-40836200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr15:40828000-40856600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:40828200-40833400	Strong transcription	Spleen	Spleen
26	chr15:40828400-40839200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr15:40828600-40839400	Weak transcription	HMEC	breast
28	chr15:40828600-40841600	Weak transcription	Colonic Mucosa	Colon
29	chr15:40828800-40839200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:40828800-40839200	Weak transcription	Liver	Liver
31	chr15:40828800-40839200	Weak transcription	Esophagus	oesophagus
32	chr15:40828800-40839400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:40829000-40841400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr15:40829200-40845200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:40829400-40839200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:40829400-40839600	Weak transcription	Fetal Brain Female	brain
37	chr15:40829400-40840800	Weak transcription	Fetal Lung	lung
38	chr15:40829400-40845000	Weak transcription	NHLF	lung
39	chr15:40829600-40835800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:40829600-40839200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:40829600-40839600	Weak transcription	Right Atrium	heart
42	chr15:40829600-40840400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:40829600-40840800	Weak transcription	Osteobl	bone
44	chr15:40829600-40845000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:40829600-40845200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr15:40829800-40833400	Strong transcription	Fetal Stomach	stomach
47	chr15:40829800-40839000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:40829800-40839200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:40829800-40839200	Weak transcription	Psoas Muscle	Psoas
50	chr15:40829800-40840800	Weak transcription	HSMMtube	muscle

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