Variant report

Variant	rs13189484
Chromosome Location	chr5:43558034-43558035
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr5:43556280-43558044	HCT-116	colon:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43555487..43559521-chr5:43598404..43605405,16	K562	blood:
2	chr5:43513317..43519979-chr5:43552519..43558793,19	K562	blood:
3	chr5:43512478..43519226-chr5:43552704..43558861,10	MCF-7	breast:
4	chr5:43482505..43485566-chr5:43554663..43558409,7	MCF-7	breast:
5	chr5:43513876..43516684-chr5:43553510..43558785,6	MCF-7	breast:
6	chr5:43481238..43485996-chr5:43553681..43560344,12	K562	blood:
7	chr5:43552832..43560830-chr5:43598877..43605844,26	MCF-7	breast:
8	chr5:43556013..43559876-chr5:43586120..43588801,3	K562	blood:
9	chr5:43479992..43486255-chr5:43553479..43560182,13	MCF-7	breast:
10	chr5:43555382..43559666-chr5:43598979..43604929,17	K562	blood:
11	chr5:43513317..43518816-chr5:43554982..43559074,7	K562	blood:
12	chr5:43554854..43559895-chr5:43599481..43606699,15	MCF-7	breast:
13	chr5:43119211..43122555-chr5:43554907..43559759,4	K562	blood:
14	chr5:43481891..43486310-chr5:43553986..43559337,13	K562	blood:

No data

Variant related genes	Relation type
PAIP1	TF binding region
ENSG00000172262	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000249286	Chromatin interaction
ENSG00000112992	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000248092	Chromatin interaction
ENSG00000151881	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10059912	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10059993	0.81[EUR][1000 genomes]
rs10065689	0.81[EUR][1000 genomes]
rs10066408	0.81[EUR][1000 genomes]
rs10068064	0.81[EUR][1000 genomes]
rs10462051	0.91[ASN][1000 genomes]
rs11949083	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11952832	0.80[EUR][1000 genomes]
rs11958046	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12332560	0.91[ASN][1000 genomes]
rs12521249	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12651879	0.89[ASN][1000 genomes]
rs12697457	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13359906	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13360902	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1366410	0.81[EUR][1000 genomes]
rs28437972	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4072918	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4072919	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4074777	0.82[EUR][1000 genomes]
rs4331909	0.87[ASN][1000 genomes]
rs4386738	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4428418	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4467713	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4535459	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4610465	0.87[EUR][1000 genomes]
rs4866833	0.87[ASN][1000 genomes]
rs4866835	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55667604	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55855322	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56008952	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56097465	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56333629	0.81[EUR][1000 genomes]
rs57403343	0.82[EUR][1000 genomes]
rs59001943	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59224335	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60297702	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6451712	0.87[ASN][1000 genomes]
rs67581152	0.89[ASN][1000 genomes]
rs6860493	0.81[EUR][1000 genomes]
rs6866325	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6866802	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6869933	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6884661	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6885679	0.83[EUR][1000 genomes]
rs6891363	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6895327	0.81[EUR][1000 genomes]
rs6898866	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7705166	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7706431	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7710628	0.83[EUR][1000 genomes]
rs7713479	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7715782	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7717636	0.91[ASN][1000 genomes]
rs7732656	0.81[EUR][1000 genomes]
rs7736615	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7737793	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9687341	0.85[ASN][1000 genomes]
rs9885189	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	esv1835614	chr5:43515280-43561759	Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	esv1837000	chr5:43515280-43561759	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	esv3471239	chr5:43541792-43587904	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	esv3471240	chr5:43541792-43587904	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	esv1792602	chr5:43556410-43561759	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	45 gene(s)	inside rSNPs	diseases
9	esv1802364	chr5:43556410-43561759	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13189484	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43554800-43558400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:43557800-43558600	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr5:43557800-43559200	Weak transcription	NHDF-Ad	bronchial
4	chr5:43557800-43559600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:43557800-43559600	Weak transcription	Fetal Heart	heart
6	chr5:43557800-43559600	Weak transcription	NHLF	lung
7	chr5:43557800-43559800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:43557800-43560200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:43557800-43560400	Weak transcription	Left Ventricle	heart
10	chr5:43557800-43561000	Weak transcription	HSMM	muscle
11	chr5:43557800-43561600	Weak transcription	HSMMtube	muscle
12	chr5:43557800-43563400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:43557800-43563400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:43557800-43571400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:43557800-43584600	Weak transcription	Psoas Muscle	Psoas
16	chr5:43558000-43558200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr5:43558000-43558200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:43558000-43558200	Enhancers	Dnd41	blood
19	chr5:43558000-43558400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr5:43558000-43558600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:43558000-43558600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr5:43558000-43559600	Weak transcription	K562	blood
23	chr5:43558000-43559800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:43558000-43559800	Weak transcription	Osteobl	bone
25	chr5:43558000-43560200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:43558000-43560200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:43558000-43560200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:43558000-43560200	Weak transcription	Hela-S3	cervix
29	chr5:43558000-43561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:43558000-43561000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr5:43558000-43561000	Weak transcription	A549	lung
32	chr5:43558000-43561800	Enhancers	GM12878-XiMat	blood
33	chr5:43558000-43563400	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:43558000-43563400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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