Variant report

Variant	rs62260830
Chromosome Location	chr3:48096735-48096736
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	chr3:48095274..48097854-chr3:48127234..48129372,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1013431	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11130152	0.80[AMR][1000 genomes]
rs11130154	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11130155	0.84[AMR][1000 genomes]
rs11710866	0.82[AMR][1000 genomes]
rs11714518	0.80[AMR][1000 genomes]
rs12486714	0.82[AMR][1000 genomes]
rs12493348	0.84[AMR][1000 genomes]
rs13074973	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13075457	0.83[AMR][1000 genomes]
rs13075795	0.82[EUR][1000 genomes]
rs13080997	0.82[AMR][1000 genomes]
rs13081463	0.80[AMR][1000 genomes]
rs1530646	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1550914	0.82[EUR][1000 genomes]
rs2053767	0.82[EUR][1000 genomes]
rs2121754	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2166770	0.82[EUR][1000 genomes]
rs2166772	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2361683	0.81[AMR][1000 genomes]
rs2361684	0.81[AMR][1000 genomes]
rs28637561	0.82[EUR][1000 genomes]
rs34597784	0.81[AMR][1000 genomes]
rs35314534	0.82[EUR][1000 genomes]
rs35689209	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4293721	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4296617	0.82[EUR][1000 genomes]
rs4392441	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4599334	0.82[EUR][1000 genomes]
rs4858876	0.80[AMR][1000 genomes]
rs4858880	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4858881	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4858887	0.83[EUR][1000 genomes]
rs5012971	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56067795	0.81[AMR][1000 genomes]
rs6442090	0.82[EUR][1000 genomes]
rs6442091	0.82[EUR][1000 genomes]
rs6442094	0.82[EUR][1000 genomes]
rs6442101	0.83[EUR][1000 genomes]
rs6770467	0.82[EUR][1000 genomes]
rs6770477	0.82[EUR][1000 genomes]
rs6773208	0.81[EUR][1000 genomes]
rs6791834	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6803741	0.84[EUR][1000 genomes]
rs6806820	0.81[EUR][1000 genomes]
rs7374516	0.82[EUR][1000 genomes]
rs7426976	0.82[EUR][1000 genomes]
rs7427418	0.82[EUR][1000 genomes]
rs7427648	0.82[AMR][1000 genomes]
rs7430879	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7430913	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7620736	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7627645	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7642590	0.86[EUR][1000 genomes]
rs7649981	0.82[EUR][1000 genomes]
rs9811277	0.82[EUR][1000 genomes]
rs9814961	0.82[EUR][1000 genomes]
rs9828959	0.80[EUR][1000 genomes]
rs9846062	0.82[EUR][1000 genomes]
rs9854454	0.82[EUR][1000 genomes]
rs9862913	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1835684	chr3:47912703-48123540	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv834681	chr3:48032000-48181775	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs62260830	ZNF589	cis	Adipose Subcutaneous	GTEx
rs62260830	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs62260830	ZNF589	cis	Nerve Tibial	GTEx
rs62260830	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs62260830	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs62260830	MRPS18AP1	cis	Nerve Tibial	GTEx
rs62260830	MRPS18AP1	cis	Artery Tibial	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48051200-48128000	Weak transcription	Primary B cells from cord blood	blood
2	chr3:48059600-48128800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:48064400-48128800	Weak transcription	Esophagus	oesophagus
4	chr3:48074800-48105400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:48075800-48102600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:48076400-48100400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:48081400-48098800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:48081400-48110600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:48081400-48128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:48081600-48099200	Weak transcription	Ovary	ovary
11	chr3:48081600-48099600	Weak transcription	Brain Anterior Caudate	brain
12	chr3:48081600-48099600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:48081600-48099800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:48081600-48100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:48081600-48100600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:48081600-48105800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:48081800-48098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:48081800-48100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:48081800-48128400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:48082000-48105600	Weak transcription	Small Intestine	intestine
21	chr3:48082200-48105800	Weak transcription	Right Ventricle	heart
22	chr3:48082200-48115000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:48083600-48099600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:48083800-48100400	Weak transcription	Right Atrium	heart
25	chr3:48084000-48111800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:48084400-48099400	Weak transcription	NH-A	brain
27	chr3:48084400-48099800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:48084400-48100000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:48086400-48100400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr3:48087600-48099800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:48089000-48099800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:48089200-48099200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:48089200-48104600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:48089400-48128400	Weak transcription	Thymus	Thymus
35	chr3:48089400-48128600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:48089600-48128400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:48089800-48128200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:48089800-48128800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:48090000-48105400	Weak transcription	NHEK	skin
40	chr3:48091000-48099200	Weak transcription	K562	blood
41	chr3:48091000-48099200	Weak transcription	NHDF-Ad	bronchial
42	chr3:48091000-48099400	Weak transcription	A549	lung
43	chr3:48091000-48099800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:48091000-48105200	Weak transcription	HSMMtube	muscle
45	chr3:48091000-48106200	Weak transcription	HUVEC	blood vessel
46	chr3:48091000-48110200	Weak transcription	HepG2	liver
47	chr3:48091200-48099200	Weak transcription	Adipose Nuclei	Adipose
48	chr3:48091200-48099600	Weak transcription	NHLF	lung
49	chr3:48091200-48099800	Weak transcription	Dnd41	blood
50	chr3:48091200-48100400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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