Variant report

Variant	rs2020383
Chromosome Location	chr5:112074356-112074357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112041577..112049243-chr5:112069735..112074802,8	K562	blood:
2	chr5:112041940..112044616-chr5:112073343..112075090,3	MCF-7	breast:
3	chr5:112041486..112046402-chr5:112068342..112076365,12	K562	blood:

Variant related genes	Relation type
ENSG00000134982	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10071425	0.83[EUR][1000 genomes]
rs10073398	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10076641	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10463643	0.86[JPT][hapmap]
rs11241182	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11241183	0.84[EUR][1000 genomes]
rs11241184	0.91[EUR][1000 genomes]
rs11241185	0.84[EUR][1000 genomes]
rs11749632	0.82[EUR][1000 genomes]
rs11749701	0.81[EUR][1000 genomes]
rs11954856	0.93[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12513804	0.93[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12518091	0.83[EUR][1000 genomes]
rs12656359	0.85[EUR][1000 genomes]
rs12659119	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12719151	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs1441375	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1465910	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1661035	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1661036	0.85[ASN][1000 genomes]
rs1816769	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1974786	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs2019720	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs2289484	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs2431239	0.84[EUR][1000 genomes]
rs2431242	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2431512	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs2431514	0.80[EUR][1000 genomes]
rs2439589	0.84[EUR][1000 genomes]
rs2439591	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2545162	0.86[CHB][hapmap]
rs2545165	0.86[CHB][hapmap]
rs2546106	0.81[CEU][hapmap]
rs2546108	0.85[CEU][hapmap]
rs2546117	0.84[EUR][1000 genomes]
rs2707763	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs2707765	0.82[EUR][1000 genomes]
rs28578275	0.84[EUR][1000 genomes]
rs2900066	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2901844	0.83[EUR][1000 genomes]
rs2909786	0.96[CEU][hapmap];0.93[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2909787	0.96[CEU][hapmap];0.93[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2909958	0.93[CEU][hapmap];0.93[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2952615	0.86[CHB][hapmap]
rs35130225	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs351771	0.93[CHB][hapmap]
rs35414976	0.84[EUR][1000 genomes]
rs3846716	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs396321	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4099181	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41115	0.93[CHB][hapmap]
rs411356	0.93[CHB][hapmap]
rs414098	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs42427	0.93[CHB][hapmap]
rs458906	0.82[EUR][1000 genomes]
rs464002	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs464708	0.86[CHB][hapmap]
rs465899	0.93[CHB][hapmap]
rs467033	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs468179	0.85[ASN][1000 genomes]
rs4705486	0.84[EUR][1000 genomes]
rs4705559	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4705608	0.84[EUR][1000 genomes]
rs4705609	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4705610	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4705624	0.84[EUR][1000 genomes]
rs4705815	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs4705816	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs544243	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs569940	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62364017	0.92[EUR][1000 genomes]
rs6594643	0.82[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6594644	0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6594646	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs6864688	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6867243	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6879057	0.84[EUR][1000 genomes]
rs6894351	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6898133	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7704618	0.81[EUR][1000 genomes]
rs861674	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs866006	0.86[CHB][hapmap]
rs9326862	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9326863	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs953916	0.82[EUR][1000 genomes]
rs9647582	0.84[EUR][1000 genomes]
rs9647583	0.84[EUR][1000 genomes]
rs971517	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830450	chr5:111964170-112134510	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv462387	chr5:112053911-112124369	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv599393	chr5:112053911-112124369	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2020383	APC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112072600-112074400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:112072600-112074600	Flanking Active TSS	Dnd41	blood
3	chr5:112072800-112074400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:112072800-112074400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr5:112072800-112074400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:112072800-112074400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr5:112072800-112074600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:112072800-112074800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:112072800-112074800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr5:112072800-112075000	Active TSS	Fetal Brain Male	brain
11	chr5:112072800-112075000	Active TSS	Fetal Brain Female	brain
12	chr5:112072800-112076400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:112073000-112074400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr5:112073000-112074400	Active TSS	Fetal Intestine Large	intestine
15	chr5:112073000-112074400	Active TSS	Fetal Intestine Small	intestine
16	chr5:112073000-112074400	Active TSS	Fetal Muscle Trunk	muscle
17	chr5:112073000-112074400	Active TSS	Right Ventricle	heart
18	chr5:112073000-112074600	Active TSS	Stomach Smooth Muscle	stomach
19	chr5:112073000-112074800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:112073000-112075000	Active TSS	Brain Anterior Caudate	brain
21	chr5:112073000-112075200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:112073000-112075400	Active TSS	NHDF-Ad	bronchial
23	chr5:112073000-112075600	Active TSS	Brain Hippocampus Middle	brain
24	chr5:112073000-112075800	Active TSS	Brain Substantia Nigra	brain
25	chr5:112073000-112076200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr5:112073000-112076200	Active TSS	NHLF	lung
27	chr5:112073200-112074400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:112073200-112075200	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr5:112073200-112076600	Active TSS	Brain Cingulate Gyrus	brain
30	chr5:112073400-112074400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:112073400-112074600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
32	chr5:112073600-112074400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
33	chr5:112073600-112074400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:112073600-112074400	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr5:112073600-112074400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr5:112073600-112074600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr5:112073800-112074400	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr5:112073800-112074400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr5:112073800-112074400	Flanking Active TSS	Fetal Stomach	stomach
40	chr5:112073800-112074400	Flanking Active TSS	Hela-S3	cervix
41	chr5:112073800-112074400	Flanking Active TSS	NHEK	skin
42	chr5:112073800-112074600	Flanking Active TSS	Fetal Lung	lung
43	chr5:112073800-112074600	Flanking Active TSS	Osteobl	bone
44	chr5:112073800-112075400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:112073800-112075400	Flanking Active TSS	HUVEC	blood vessel
46	chr5:112073800-112086800	Weak transcription	Gastric	stomach
47	chr5:112074000-112074400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
48	chr5:112074000-112074400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:112074000-112074400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:112074000-112074400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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