Variant report

Variant	rs28860492
Chromosome Location	chr15:41818060-41818061
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	chr15:41812182..41819156-chr15:41830894..41838104,9	K562	blood:
2	chr15:41811420..41814118-chr15:41817482..41820204,2	K562	blood:

Variant related genes	Relation type
ENSG00000103932	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11070334	0.83[EUR][1000 genomes]
rs11632399	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1200345	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200346	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1200348	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1200349	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274858	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289740	0.81[ASN][1000 genomes]
rs2297378	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2297380	0.84[EUR][1000 genomes]
rs7178957	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][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	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv471241	chr15:41783814-41820200	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904112	chr15:41806658-41836234	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv569234	chr15:41815649-41822302	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28860492	LTK	cis	lung	GTEx
rs28860492	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs28860492	TYRO3	cis	lung	GTEx
rs28860492	RPAP1	cis	Artery Tibial	GTEx
rs28860492	RPAP1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41801800-41819000	Weak transcription	Hela-S3	cervix
2	chr15:41806200-41820400	Weak transcription	HSMM	muscle
3	chr15:41806200-41822600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:41806400-41818600	Weak transcription	Primary B cells from cord blood	blood
5	chr15:41806400-41835200	Weak transcription	Right Atrium	heart
6	chr15:41806600-41818800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:41806600-41818800	Weak transcription	GM12878-XiMat	blood
8	chr15:41806600-41819000	Weak transcription	HUVEC	blood vessel
9	chr15:41806600-41819200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:41806600-41824600	Weak transcription	Fetal Kidney	kidney
11	chr15:41806600-41835200	Weak transcription	Fetal Heart	heart
12	chr15:41806800-41818200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:41806800-41818400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:41806800-41818600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:41806800-41818800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:41806800-41818800	Weak transcription	Stomach Mucosa	stomach
17	chr15:41806800-41822400	Weak transcription	NH-A	brain
18	chr15:41807200-41819400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:41807200-41835600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:41808000-41829600	Strong transcription	Fetal Stomach	stomach
21	chr15:41808200-41818200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:41808200-41820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:41808600-41823000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:41808600-41829200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr15:41808600-41829600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:41808600-41835400	Weak transcription	Fetal Brain Male	brain
27	chr15:41808800-41829600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:41809000-41829400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:41809000-41829400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:41809600-41829200	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:41809600-41829400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:41809800-41818600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:41810000-41820400	Weak transcription	Small Intestine	intestine
34	chr15:41810200-41818400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:41810200-41819000	Weak transcription	HSMMtube	muscle
36	chr15:41810400-41818600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:41810400-41819400	Weak transcription	Psoas Muscle	Psoas
38	chr15:41810600-41818600	Weak transcription	HMEC	breast
39	chr15:41810600-41818800	Weak transcription	K562	blood
40	chr15:41811400-41818600	Weak transcription	HepG2	liver
41	chr15:41811400-41819200	Weak transcription	A549	lung
42	chr15:41811600-41829600	Strong transcription	Fetal Intestine Large	intestine
43	chr15:41811600-41829800	Strong transcription	Fetal Muscle Leg	muscle
44	chr15:41811800-41829400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:41811800-41829400	Strong transcription	Brain Hippocampus Middle	brain
46	chr15:41811800-41829400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr15:41811800-41829600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:41811800-41829600	Strong transcription	Brain Anterior Caudate	brain
49	chr15:41812000-41822800	Strong transcription	Placenta	Placenta
50	chr15:41812000-41823200	Strong transcription	Adipose Nuclei	Adipose

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