Variant report

Variant	rs13126596
Chromosome Location	chr4:120140729-120140730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:120138762..120140367-chr4:120140533..120142369,2	K562	blood:
2	chr4:120132080..120136189-chr4:120136407..120141066,11	MCF-7	breast:
3	chr4:120136237..120140737-chr4:120147652..120152174,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP53-1	chr4:120138705-120142650	NONHSAT098036

Variant related genes	Relation type
ENSG00000178636	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10006304	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10006877	0.82[AMR][1000 genomes]
rs10010696	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10013032	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10022262	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10022508	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029750	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10031033	0.87[EUR][1000 genomes]
rs1011054	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10213342	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1022145	0.82[AMR][1000 genomes]
rs1033087	0.90[ASN][1000 genomes]
rs11098490	0.87[ASN][1000 genomes]
rs11098491	0.87[ASN][1000 genomes]
rs11098492	0.89[ASN][1000 genomes]
rs11098493	0.90[ASN][1000 genomes]
rs11098496	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11098499	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11722872	0.80[AMR][1000 genomes]
rs11726229	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11729897	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11733239	0.86[ASN][1000 genomes]
rs11734519	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11931312	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11944880	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12186259	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12499598	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12501610	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12502503	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12505469	0.82[AMR][1000 genomes]
rs12506395	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12509054	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12512517	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12513191	0.89[ASN][1000 genomes]
rs13113112	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13114751	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13116504	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13120560	0.87[ASN][1000 genomes]
rs13123591	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13129661	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13133044	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13136593	0.89[ASN][1000 genomes]
rs13138782	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13435802	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1397608	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1511015	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1511018	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1511019	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1546502	0.82[AMR][1000 genomes]
rs1546505	0.80[AMR][1000 genomes]
rs1551	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17839089	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017057	0.82[AMR][1000 genomes]
rs2036861	0.90[ASN][1000 genomes]
rs2203039	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28374891	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28419773	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28452522	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28555550	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34585914	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34616304	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34630083	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35197422	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35271032	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35434465	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35643470	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35916640	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3749591	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4145951	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4355373	0.87[ASN][1000 genomes]
rs4833612	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4833613	0.86[ASN][1000 genomes]
rs56122576	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56386062	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6534130	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67073020	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs68128210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814412	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6815725	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6822498	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6826823	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6832670	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6837898	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6838674	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6845702	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6847248	0.81[AMR][1000 genomes]
rs6849889	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6851130	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6851169	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72676045	0.80[AMR][1000 genomes]
rs7441137	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7659194	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7661020	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7672493	0.81[AMR][1000 genomes]
rs7684942	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7685268	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs878373	0.82[AMR][1000 genomes]
rs951570	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9884728	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9993110	0.88[ASN][1000 genomes]
rs9995277	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9996382	0.86[EUR][1000 genomes];0.97[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	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	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	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
5	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13126596	RP11-384K6.6	cis	Whole Blood	GTEx
rs13126596	RP11-33B1.1	cis	lung	GTEx
rs13126596	RP11-384K6.6	cis	Artery Tibial	GTEx
rs13126596	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs13126596	RP11-33B1.1	cis	Whole Blood	GTEx
rs13126596	RP11-33B1.1	cis	Nerve Tibial	GTEx
rs13126596	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120134600-120144600	Weak transcription	Spleen	Spleen
2	chr4:120134800-120142000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:120134800-120143400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:120134800-120147000	Weak transcription	Fetal Brain Male	brain
5	chr4:120134800-120170000	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:120135000-120142600	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:120135000-120142800	Weak transcription	Lung	lung
8	chr4:120135000-120154800	Weak transcription	Primary B cells from cord blood	blood
9	chr4:120135000-120170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:120135000-120195800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:120135200-120142000	Weak transcription	Esophagus	oesophagus
12	chr4:120135200-120142000	Weak transcription	Ovary	ovary
13	chr4:120135200-120143200	Weak transcription	Brain Substantia Nigra	brain
14	chr4:120135200-120143600	Weak transcription	Thymus	Thymus
15	chr4:120135200-120155000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:120135200-120155000	Weak transcription	Small Intestine	intestine
17	chr4:120135200-120163600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:120135200-120176200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:120135200-120176200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:120135400-120142400	Weak transcription	Fetal Intestine Small	intestine
21	chr4:120135400-120159000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:120135400-120194600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:120135600-120141800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr4:120135600-120142200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:120135600-120142800	Weak transcription	Fetal Stomach	stomach
26	chr4:120135600-120155000	Weak transcription	K562	blood
27	chr4:120135600-120173800	Weak transcription	Brain Anterior Caudate	brain
28	chr4:120136000-120145600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr4:120136200-120143000	Weak transcription	NH-A	brain
30	chr4:120136200-120147400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr4:120136200-120148000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:120136200-120154400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
34	chr4:120136400-120151600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:120136400-120155000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr4:120136400-120155000	Weak transcription	Stomach Mucosa	stomach
37	chr4:120136400-120156400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:120136600-120142800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:120136800-120142200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:120137000-120151000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:120137400-120155000	Weak transcription	Right Atrium	heart
42	chr4:120137600-120154600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr4:120138000-120141000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
44	chr4:120138400-120141000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:120138400-120141000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:120138400-120144400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:120138400-120144600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr4:120138400-120144800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr4:120138600-120143800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr4:120138600-120148000	Weak transcription	Pancreas	Pancrea

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