Variant report

Variant	rs56267974
Chromosome Location	chr15:45715360-45715361
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	chr15:45714078..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: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10152337	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10152697	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12324848	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1288861	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16942066	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1706799	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17533116	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17533716	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17535381	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17537244	0.98[ASN][1000 genomes]
rs17618294	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2433602	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453546	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2461706	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486287	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668746	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55721266	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55904415	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56273246	0.98[ASN][1000 genomes]
rs56306977	1.00[AMR][1000 genomes];1.00[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	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57419781	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61301536	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709081	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72709084	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72709088	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72709089	0.80[AMR][1000 genomes]
rs72709092	0.88[AMR][1000 genomes]
rs72711253	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711255	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711259	0.98[ASN][1000 genomes]
rs9972405	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9972498	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9972528	1.00[AMR][1000 genomes];0.98[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
rs56267974	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	chr15:45696600-45718400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:45697000-45722200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:45697400-45716000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:45697400-45716200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:45697400-45716400	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr15:45697600-45715800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr15:45697800-45715400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:45697800-45716000	Strong transcription	Duodenum Mucosa	Duodenum
9	chr15:45697800-45716400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr15:45698600-45716200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:45699200-45715400	Strong transcription	Brain Germinal Matrix	brain
12	chr15:45706200-45722600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:45706600-45722800	Weak transcription	Fetal Heart	heart
14	chr15:45707000-45715400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:45708000-45715600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:45708200-45716000	Strong transcription	Primary B cells from cord blood	blood
17	chr15:45710000-45715400	Strong transcription	Fetal Intestine Large	intestine
18	chr15:45710000-45720600	Weak transcription	A549	lung
19	chr15:45710800-45716000	Strong transcription	GM12878-XiMat	blood
20	chr15:45711000-45719000	Weak transcription	Fetal Brain Male	brain
21	chr15:45711400-45722400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:45711400-45722600	Weak transcription	Brain Substantia Nigra	brain
23	chr15:45711600-45720800	Weak transcription	Small Intestine	intestine
24	chr15:45711600-45722400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:45711600-45722400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:45711800-45716800	Weak transcription	Fetal Kidney	kidney
27	chr15:45711800-45722200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:45711800-45722200	Weak transcription	Stomach Mucosa	stomach
29	chr15:45711800-45722400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:45711800-45722400	Weak transcription	Pancreas	Pancrea
31	chr15:45711800-45722600	Weak transcription	Spleen	Spleen
32	chr15:45712000-45717200	Weak transcription	Aorta	Aorta
33	chr15:45712000-45718600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:45712000-45719800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:45712000-45722200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:45712000-45722200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:45712000-45722400	Weak transcription	Brain Angular Gyrus	brain
38	chr15:45712000-45722400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr15:45712000-45722400	Weak transcription	Gastric	stomach
40	chr15:45712000-45722600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:45712000-45722600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:45712000-45722600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr15:45712000-45722600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:45712200-45721600	Weak transcription	Esophagus	oesophagus
45	chr15:45712200-45721600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr15:45712200-45722200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:45712200-45722400	Weak transcription	Brain Hippocampus Middle	brain
48	chr15:45712200-45722400	Weak transcription	Lung	lung
49	chr15:45712200-45722400	Weak transcription	Ovary	ovary
50	chr15:45712200-45722600	Weak transcription	Colonic Mucosa	Colon

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