Variant report

Variant	rs549002
Chromosome Location	chr1:169890041-169890042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169887846..169894353-chr1:169898169..169903456,7	K562	blood:
2	chr1:169863260..169865221-chr1:169889034..169890676,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10489172	0.82[AMR][1000 genomes]
rs1062976	0.82[AMR][1000 genomes]
rs10919255	0.82[AMR][1000 genomes]
rs10919267	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11589247	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12064636	0.82[AMR][1000 genomes]
rs12089057	0.82[AMR][1000 genomes]
rs12760399	0.82[AMR][1000 genomes]
rs1541160	0.84[AFR][1000 genomes]
rs16862745	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17529513	0.81[AMR][1000 genomes]
rs17603022	0.82[AMR][1000 genomes]
rs2474708	0.82[AFR][1000 genomes]
rs28441321	0.84[AFR][1000 genomes]
rs516793	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527261	0.87[AFR][1000 genomes]
rs541896	0.84[AFR][1000 genomes]
rs546894	0.87[AFR][1000 genomes]
rs614044	0.84[AFR][1000 genomes]
rs621437	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628436	0.84[AFR][1000 genomes]
rs629421	1.00[JPT][hapmap]
rs648576	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659476	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678351	0.82[AMR][1000 genomes]
rs6694855	0.85[AMR][1000 genomes]
rs73026213	0.85[AMR][1000 genomes]
rs73026243	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73026245	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7539241	0.81[AFR][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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs549002	KIFAP3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169876200-169903600	Weak transcription	Aorta	Aorta
2	chr1:169878400-169892200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:169878400-169895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:169878600-169895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:169880200-169892800	Weak transcription	Fetal Heart	heart
7	chr1:169881400-169901000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:169882200-169892000	Weak transcription	Brain Germinal Matrix	brain
9	chr1:169883000-169890600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:169884200-169913000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:169884400-169891000	Weak transcription	Esophagus	oesophagus
12	chr1:169884600-169892800	Weak transcription	Pancreas	Pancrea
13	chr1:169884600-169895200	Weak transcription	Fetal Intestine Small	intestine
14	chr1:169884600-169900600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:169884600-169900600	Weak transcription	NHDF-Ad	bronchial
16	chr1:169885200-169900800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:169885400-169894000	Weak transcription	Right Ventricle	heart
18	chr1:169885400-169913200	Weak transcription	Ovary	ovary
19	chr1:169885600-169892200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:169885600-169903200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:169885800-169896600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:169885800-169898000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:169886000-169894000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:169886400-169894600	Weak transcription	Primary B cells from cord blood	blood
25	chr1:169886400-169895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:169886400-169913000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:169886600-169915600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:169886800-169891000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:169887000-169911400	Weak transcription	Left Ventricle	heart
30	chr1:169888200-169891000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:169888200-169891000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:169888200-169891000	Strong transcription	Adipose Nuclei	Adipose
33	chr1:169888400-169890200	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:169888400-169891000	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:169888400-169892400	Weak transcription	Fetal Brain Male	brain
36	chr1:169888600-169891400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:169888600-169891400	Weak transcription	Liver	Liver
38	chr1:169888800-169894800	Weak transcription	GM12878-XiMat	blood
39	chr1:169888800-169900600	Weak transcription	Fetal Stomach	stomach
40	chr1:169889000-169890200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:169889000-169890800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:169889000-169895200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:169889400-169890200	Weak transcription	Primary T cells from cord blood	blood
44	chr1:169889400-169891400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:169889600-169900600	Weak transcription	Fetal Lung	lung
46	chr1:169889800-169898000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:169890000-169890800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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