Variant report

Variant	rs2839963
Chromosome Location	chr1:45732314-45732315
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45716599..45723837-chr1:45726714..45733883,8	K562	blood:
2	chr1:45732068..45734921-chr1:45735419..45738546,3	K562	blood:
3	chr1:45476441..45479268-chr1:45730943..45735268,3	K562	blood:
4	chr1:45731206..45733732-chr1:45740746..45742362,2	K562	blood:
5	chr1:45284070..45285582-chr1:45729873..45732531,2	K562	blood:
6	chr1:45730564..45732542-chr1:45986533..45988219,2	K562	blood:

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000117450	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10789459	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211076	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11211086	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024401	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12031333	1.00[JPT][hapmap]
rs12033111	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3009977	1.00[JPT][hapmap]
rs72684475	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7513367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7522177	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
4	nsv998187	chr1:45677251-45732377	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2839963	SKAP2	trans	lymphoblastoid	seeQTL
rs2839963	NASP	cis	parietal	SCAN
rs2839963	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs2839963	MUTYH	cis	lymphoblastoid	seeQTL
rs2839963	UROD	cis	multi-tissue	Pritchard

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45730400-45732800	Enhancers	Duodenum Mucosa	Duodenum
2	chr1:45730600-45732600	Weak transcription	Small Intestine	intestine
3	chr1:45730800-45732400	Enhancers	Colonic Mucosa	Colon
4	chr1:45731000-45732400	Enhancers	Brain Hippocampus Middle	brain
5	chr1:45731000-45732400	Enhancers	Fetal Intestine Large	intestine
6	chr1:45731000-45732400	Enhancers	Stomach Mucosa	stomach
7	chr1:45731000-45732600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:45731000-45733400	Enhancers	Fetal Intestine Small	intestine
9	chr1:45731000-45733600	Enhancers	HUVEC	blood vessel
10	chr1:45731200-45732800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:45731400-45732400	Enhancers	Pancreas	Pancrea
12	chr1:45731400-45732400	Enhancers	Right Atrium	heart
13	chr1:45731400-45732600	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr1:45731600-45732400	Enhancers	Adipose Nuclei	Adipose
15	chr1:45731600-45732400	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr1:45731600-45732600	Enhancers	Colon Smooth Muscle	Colon
17	chr1:45731600-45733000	Enhancers	NHLF	lung
18	chr1:45731600-45733600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:45731800-45732400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:45731800-45732400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr1:45731800-45732400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:45731800-45732400	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr1:45731800-45732400	Flanking Active TSS	A549	lung
24	chr1:45731800-45732600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:45731800-45732600	Enhancers	HMEC	breast
26	chr1:45731800-45732600	Flanking Active TSS	K562	blood
27	chr1:45731800-45732600	Flanking Active TSS	NH-A	brain
28	chr1:45731800-45732800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:45731800-45734200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:45732000-45732400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:45732000-45732400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:45732000-45732400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:45732000-45732400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:45732000-45732400	Enhancers	Fetal Kidney	kidney
35	chr1:45732000-45732400	Enhancers	Rectal Smooth Muscle	rectum
36	chr1:45732000-45732400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr1:45732000-45732400	Enhancers	HSMMtube	muscle
38	chr1:45732200-45732400	Flanking Active TSS	Hela-S3	cervix
39	chr1:45732200-45732400	Flanking Active TSS	HepG2	liver
40	chr1:45732200-45732600	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:45732200-45733200	Weak transcription	Ovary	ovary
42	chr1:45732200-45733400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr1:45732200-45733600	Enhancers	Osteobl	bone

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