Variant report

Variant	rs11734519
Chromosome Location	chr4:120171071-120171072
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	chr4:119991797..119993940-chr4:120168867..120171491,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10003567	0.81[ASN][1000 genomes]
rs10005237	0.81[ASN][1000 genomes]
rs10006304	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10006877	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10010696	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10022262	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10029750	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10031033	0.86[ASN][1000 genomes]
rs10032299	0.84[ASN][1000 genomes]
rs1011054	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10212775	0.81[ASN][1000 genomes]
rs10213267	0.81[ASN][1000 genomes]
rs10213342	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1022145	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1052633	0.82[ASN][1000 genomes]
rs11098496	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098497	0.85[ASN][1000 genomes]
rs11098498	0.85[ASN][1000 genomes]
rs11098499	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11722872	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11726229	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11729897	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732087	0.81[ASN][1000 genomes]
rs11732621	0.83[ASN][1000 genomes]
rs11931312	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11944880	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12186259	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12499598	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12501610	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12505469	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12506395	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12506610	0.81[ASN][1000 genomes]
rs12510269	0.81[ASN][1000 genomes]
rs12512517	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12711071	0.81[ASN][1000 genomes]
rs13113112	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114751	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13116504	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13126596	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13129661	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13133044	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13138782	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13139045	0.99[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13435802	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1397608	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1511015	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1511018	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1511019	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1511025	0.81[ASN][1000 genomes]
rs1546502	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1546504	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1546505	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1551	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2017057	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2175383	0.82[ASN][1000 genomes]
rs28374891	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28419773	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28555550	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28652763	0.81[ASN][1000 genomes]
rs2964	0.81[ASN][1000 genomes]
rs34585914	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34616304	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34630083	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35197422	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35271032	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35434465	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35643470	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35916640	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3749591	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4145951	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4472123	0.81[ASN][1000 genomes]
rs56122576	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56386062	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67073020	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68128210	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6814412	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6815725	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6822808	0.82[ASN][1000 genomes]
rs6837898	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6843509	0.80[ASN][1000 genomes]
rs6847248	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6849889	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6857105	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs714899	0.81[ASN][1000 genomes]
rs72676045	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7659194	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7659403	0.84[ASN][1000 genomes]
rs7672493	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7684942	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7685268	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878373	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs878376	0.81[ASN][1000 genomes]
rs9991166	0.81[ASN][1000 genomes]
rs9996494	0.81[ASN][1000 genomes]
rs9996644	0.81[ASN][1000 genomes]
rs9999724	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
5	esv2763386	chr4:120143861-120186968	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv461632	chr4:120158734-120180790	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv461633	chr4:120158734-120180790	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv595332	chr4:120158734-120180790	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11734519	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs11734519	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs11734519	RP11-33B1.1	cis	lung	GTEx
rs11734519	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs11734519	RP11-33B1.1	cis	Whole Blood	GTEx
rs11734519	RP11-33B1.1	cis	Heart Left Ventricle	GTEx
rs11734519	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs11734519	RP11-384K6.6	cis	Whole Blood	GTEx

Chromatin state (count:106 , 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	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
6	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
7	chr4:120141000-120192400	Weak transcription	Hela-S3	cervix
8	chr4:120143000-120176200	Weak transcription	Esophagus	oesophagus
9	chr4:120146000-120178600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:120148200-120213600	Weak transcription	Fetal Muscle Leg	muscle
11	chr4:120155400-120176200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:120155400-120176400	Weak transcription	Right Ventricle	heart
13	chr4:120155600-120173800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:120155600-120176400	Weak transcription	Brain Substantia Nigra	brain
15	chr4:120155600-120186000	Weak transcription	Fetal Heart	heart
16	chr4:120157600-120176800	Weak transcription	Primary B cells from cord blood	blood
17	chr4:120159400-120200800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:120159400-120201600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:120159400-120206200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:120159600-120200800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:120159800-120188400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:120160400-120174200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:120160800-120195000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:120161000-120173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:120162400-120176600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:120163800-120175600	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:120164000-120176600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:120164600-120173000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:120165000-120171400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:120165600-120172400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr4:120165800-120172000	Strong transcription	NHDF-Ad	bronchial
32	chr4:120165800-120179400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:120165800-120187000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr4:120166000-120183600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:120166000-120195200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:120166200-120171400	Strong transcription	Osteobl	bone
37	chr4:120166200-120172000	Weak transcription	Brain Germinal Matrix	brain
38	chr4:120166200-120175000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr4:120166200-120175200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:120166400-120173600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:120166400-120175800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr4:120166400-120180600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:120166400-120187200	Weak transcription	Fetal Kidney	kidney
44	chr4:120166400-120189800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:120166400-120206200	Weak transcription	Small Intestine	intestine
46	chr4:120166600-120172000	Strong transcription	HSMM	muscle
47	chr4:120166600-120172000	Strong transcription	HUVEC	blood vessel
48	chr4:120167000-120171600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr4:120167000-120171600	Strong transcription	NHEK	skin
50	chr4:120167000-120172200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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