Variant report

Variant	rs12499598
Chromosome Location	chr4:120189303-120189304
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	chr4:120182924..120185910-chr4:120187445..120191655,4	K562	blood:

Variant related genes	Relation type
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10006304	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10006877	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10010696	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10012456	0.80[AMR][1000 genomes]
rs10022262	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10029750	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10031033	0.83[ASN][1000 genomes]
rs10032299	0.82[ASN][1000 genomes]
rs1011054	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10213342	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1022145	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11098496	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11098497	0.82[ASN][1000 genomes]
rs11098498	0.82[ASN][1000 genomes]
rs11098499	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11722872	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11726229	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11729897	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732621	0.80[ASN][1000 genomes]
rs11734519	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11931312	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11944880	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12186259	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12501610	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12505469	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12506395	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12512517	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13113112	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13114751	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13116504	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13126596	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13129661	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13133044	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13138782	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13139045	0.82[EUR][1000 genomes]
rs13435802	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1397608	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1511015	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1511018	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1511019	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1546502	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1546504	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1546505	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1551	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2017057	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28374891	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28419773	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28555550	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34585914	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34616304	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34630083	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35197422	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35271032	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35434465	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35643470	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35916640	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3749591	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4145951	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56122576	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56386062	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67073020	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68128210	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6814412	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6815725	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6837898	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847075	0.80[AMR][1000 genomes]
rs6847248	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6849889	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6857105	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72676045	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7659194	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7659403	0.82[ASN][1000 genomes]
rs7672493	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7684942	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7685268	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs878373	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription 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	58 gene(s)	inside rSNPs	diseases
4	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS 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	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12499598	RP11-33B1.1	cis	Whole Blood	GTEx
rs12499598	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs12499598	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs12499598	RP11-384K6.6	cis	Whole Blood	GTEx
rs12499598	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs12499598	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs12499598	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs12499598	RP11-33B1.1	cis	lung	GTEx
rs12499598	RP11-33B1.1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
4	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
5	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:120159400-120200800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:120159400-120201600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:120159400-120206200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:120159600-120200800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:120160800-120195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:120166000-120195200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:120166400-120189800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:120166400-120206200	Weak transcription	Small Intestine	intestine
14	chr4:120167000-120194400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:120167800-120192400	Weak transcription	Psoas Muscle	Psoas
16	chr4:120170600-120192600	Weak transcription	Fetal Thymus	thymus
17	chr4:120170600-120206200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:120173400-120195200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:120174200-120191800	Weak transcription	Fetal Lung	lung
20	chr4:120174200-120192600	Weak transcription	Brain Anterior Caudate	brain
21	chr4:120174400-120191600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:120174400-120206200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:120175400-120189400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:120175600-120195200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr4:120176800-120192200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:120176800-120193400	Strong transcription	NHDF-Ad	bronchial
27	chr4:120176800-120194400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:120176800-120200800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:120176800-120202600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:120177000-120191600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:120177000-120192600	Weak transcription	Gastric	stomach
32	chr4:120177000-120194800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:120177000-120195000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:120177000-120205600	Weak transcription	Aorta	Aorta
35	chr4:120177000-120206000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr4:120177000-120213600	Weak transcription	Lung	lung
37	chr4:120177000-120220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:120177000-120220200	Weak transcription	Pancreas	Pancrea
39	chr4:120177200-120189400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:120177200-120206200	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:120177200-120213600	Weak transcription	Esophagus	oesophagus
42	chr4:120177800-120211400	Weak transcription	HepG2	liver
43	chr4:120178200-120192400	Weak transcription	NH-A	brain
44	chr4:120178200-120213400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr4:120178200-120213600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:120178200-120213800	Weak transcription	Primary B cells from cord blood	blood
47	chr4:120178400-120192600	Weak transcription	Ovary	ovary
48	chr4:120178600-120189600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:120178600-120192400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:120178600-120206200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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