Variant report

Variant	rs12565875
Chromosome Location	chr1:224425165-224425166
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224420004..224422036-chr1:224423649..224426323,3	K562	blood:

Variant related genes	Relation type
ENSG00000143748	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10916470	0.83[CEU][hapmap]
rs10916514	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1401320	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2139155	0.88[CEU][hapmap];0.82[GIH][hapmap];0.91[MKK][hapmap]
rs35584106	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6689187	0.92[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7543863	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
2	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12565875	FBXO28	cis	lymphoblastoid	seeQTL
rs12565875	FBXO28	cis	multi-tissue	Pritchard
rs12565875	DEGS1	cis	cerebellum	SCAN
rs12565875	FBXO28	Cis_1M	lymphoblastoid	RTeQTL
rs12565875	RAB3GAP2	cis	parietal	SCAN
rs12565875	DEGS1	cis	multi-tissue	Pritchard
rs12565875	RP11-365O16.3	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	chr1:224401800-224427600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224401800-224475400	Weak transcription	Esophagus	oesophagus
3	chr1:224407600-224434000	Weak transcription	Fetal Brain Male	brain
4	chr1:224411600-224438000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:224411600-224454400	Weak transcription	Psoas Muscle	Psoas
6	chr1:224412000-224433000	Weak transcription	Fetal Heart	heart
7	chr1:224412400-224473600	Weak transcription	HepG2	liver
8	chr1:224413200-224432600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:224413800-224428000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:224413800-224428200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr1:224414000-224432200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:224414200-224426200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:224414200-224427800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:224414200-224427800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:224414200-224428800	Strong transcription	Fetal Intestine Large	intestine
16	chr1:224414200-224438000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:224414400-224428800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:224414600-224426200	Strong transcription	Fetal Intestine Small	intestine
19	chr1:224415000-224436200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:224415000-224440000	Weak transcription	Fetal Kidney	kidney
21	chr1:224415600-224426000	Weak transcription	Brain Substantia Nigra	brain
22	chr1:224415600-224426400	Strong transcription	Fetal Stomach	stomach
23	chr1:224415600-224432600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:224415600-224435000	Weak transcription	Gastric	stomach
25	chr1:224415800-224435600	Weak transcription	NHLF	lung
26	chr1:224415800-224435800	Weak transcription	Brain Angular Gyrus	brain
27	chr1:224416000-224426000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:224416000-224432800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:224416000-224436600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:224416000-224465600	Weak transcription	Small Intestine	intestine
31	chr1:224416200-224433000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:224417200-224427600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:224417200-224427600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:224417400-224426400	Strong transcription	Dnd41	blood
35	chr1:224417400-224427600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:224417400-224427800	Strong transcription	Primary T cells from cord blood	blood
37	chr1:224417400-224427800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:224417600-224426800	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:224417800-224425400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:224417800-224435600	Weak transcription	Colonic Mucosa	Colon
41	chr1:224418000-224426000	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:224418000-224435400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:224418000-224436600	Weak transcription	Right Ventricle	heart
44	chr1:224418400-224439400	Weak transcription	HSMMtube	muscle
45	chr1:224419200-224432600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:224419200-224435600	Weak transcription	Brain Anterior Caudate	brain
47	chr1:224419200-224436600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:224419400-224427200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:224420400-224426200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:224420400-224427800	Strong transcription	Fetal Muscle Leg	muscle

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