Variant report

Variant	rs2486287
Chromosome Location	chr15:45714320-45714321
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45714078..45715675-chr15:45721570..45724241,2	K562	blood:
2	chr15:45713167..45716395-chr15:45719054..45724241,4	K562	blood:

Variant related genes	Relation type
ENSG00000166920	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10152337	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10152697	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10851425	1.00[CHB][hapmap]
rs1145073	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1145094	0.81[YRI][hapmap]
rs1153830	0.88[CHB][hapmap]
rs1153831	0.88[CHB][hapmap]
rs1153832	0.88[CHB][hapmap]
rs1153850	0.81[YRI][hapmap]
rs12324848	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1288861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1288863	1.00[CHB][hapmap]
rs1288865	1.00[CHB][hapmap]
rs16941238	1.00[JPT][hapmap]
rs16942066	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16944629	0.88[CHB][hapmap]
rs16952731	0.88[CHB][hapmap]
rs1706799	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17533116	0.83[EUR][1000 genomes]
rs17533716	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17535381	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17537244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17618294	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1874318	0.86[AFR][1000 genomes]
rs2088164	0.88[CHB][hapmap]
rs2217121	0.80[YRI][hapmap]
rs2433229	0.83[JPT][hapmap]
rs2433600	0.88[CHB][hapmap]
rs2433602	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433604	0.81[YRI][hapmap]
rs2433605	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2433606	0.92[AFR][1000 genomes]
rs2453546	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2461706	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467856	0.88[AFR][1000 genomes]
rs2467857	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2486289	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2486290	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs2668746	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4448883	0.88[CHB][hapmap]
rs55721266	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55904415	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56267974	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56273246	0.98[ASN][1000 genomes]
rs56306977	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56327050	0.98[ASN][1000 genomes]
rs56937414	0.96[ASN][1000 genomes]
rs56967490	0.98[ASN][1000 genomes]
rs57369693	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57419781	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61301536	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493157	0.88[CHB][hapmap]
rs6493158	0.88[CHB][hapmap]
rs7165838	0.86[CHB][hapmap]
rs7173983	0.88[CHB][hapmap]
rs72709081	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72709084	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72709088	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711253	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711255	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711259	0.98[ASN][1000 genomes]
rs8023437	0.88[CHB][hapmap]
rs8042811	0.88[CHB][hapmap]
rs9972405	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9972498	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9972528	0.96[EUR][1000 genomes];0.98[ASN][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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2486287	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45696600-45715000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
2	chr15:45696600-45718400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:45696800-45714800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:45697000-45722200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:45697200-45715200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:45697200-45715200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:45697400-45714600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr15:45697400-45714800	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:45697400-45715200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:45697400-45715200	Strong transcription	Adipose Nuclei	Adipose
11	chr15:45697400-45716000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:45697400-45716200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:45697400-45716400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr15:45697600-45714800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:45697600-45715200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr15:45697600-45715200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:45697600-45715200	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:45697600-45715200	Strong transcription	Fetal Thymus	thymus
19	chr15:45697600-45715800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:45697800-45714600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:45697800-45714800	Strong transcription	Stomach Smooth Muscle	stomach
22	chr15:45697800-45715000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:45697800-45715000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:45697800-45715400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:45697800-45716000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr15:45697800-45716400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr15:45698000-45714600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:45698000-45715200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:45698000-45715200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:45698600-45716200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:45699200-45714800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:45699200-45715400	Strong transcription	Brain Germinal Matrix	brain
33	chr15:45700400-45714800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:45700800-45714800	Strong transcription	HSMMtube	muscle
35	chr15:45704800-45714800	Strong transcription	NH-A	brain
36	chr15:45706200-45714800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:45706200-45722600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:45706600-45714800	Strong transcription	Liver	Liver
39	chr15:45706600-45714800	Strong transcription	Hela-S3	cervix
40	chr15:45706600-45722800	Weak transcription	Fetal Heart	heart
41	chr15:45706800-45714800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:45707000-45714800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr15:45707000-45714800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr15:45707000-45714800	Strong transcription	Dnd41	blood
45	chr15:45707000-45714800	Strong transcription	HUVEC	blood vessel
46	chr15:45707000-45715000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:45707000-45715000	Strong transcription	HepG2	liver
48	chr15:45707000-45715200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr15:45707000-45715200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:45707000-45715400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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