Variant report

Variant	rs56097465
Chromosome Location	chr5:43563100-43563101
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43562535..43565589-chr5:43568381..43570890,3	K562	blood:
2	chr5:43562817..43565608-chr5:43599983..43604180,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112992	Chromatin interaction
ENSG00000248092	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10036954	0.82[ASN][1000 genomes]
rs10053229	0.82[ASN][1000 genomes]
rs10059912	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10059993	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10065689	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10066408	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10068064	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10462051	0.94[ASN][1000 genomes]
rs11949083	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11952832	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11958046	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12332560	0.94[ASN][1000 genomes]
rs12521249	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12651879	0.92[ASN][1000 genomes]
rs12697457	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13189484	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13359906	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13360902	0.89[EUR][1000 genomes]
rs1366410	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28437972	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28606458	0.84[ASN][1000 genomes]
rs3776423	0.82[ASN][1000 genomes]
rs4072918	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4072919	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4074777	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4331909	0.90[ASN][1000 genomes]
rs4386738	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4428418	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4467713	0.90[ASN][1000 genomes]
rs4535459	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4610465	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4866833	0.90[ASN][1000 genomes]
rs4866835	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55667604	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55855322	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56008952	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56333629	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57403343	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59001943	0.90[ASN][1000 genomes]
rs59224335	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60297702	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6451712	0.90[ASN][1000 genomes]
rs67261887	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67466542	0.82[ASN][1000 genomes]
rs67581152	0.92[ASN][1000 genomes]
rs6860493	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6866325	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6866802	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6869933	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6884661	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6885679	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6891363	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6895327	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6898866	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72756535	0.82[ASN][1000 genomes]
rs7705166	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7706431	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7710628	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7713479	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7715782	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7717636	0.94[ASN][1000 genomes]
rs7732656	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7736615	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7737793	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9687341	0.85[ASN][1000 genomes]
rs9885189	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	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	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56097465	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43557800-43563400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:43557800-43563400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:43557800-43571400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr5:43557800-43584600	Weak transcription	Psoas Muscle	Psoas
5	chr5:43558000-43563400	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:43558000-43563400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:43560200-43584400	Weak transcription	K562	blood
8	chr5:43561000-43564600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:43561200-43565400	Weak transcription	HepG2	liver
10	chr5:43562000-43570400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:43562200-43563400	Weak transcription	NHLF	lung
12	chr5:43562200-43563400	Weak transcription	Osteobl	bone
13	chr5:43562400-43563400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:43562800-43563200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:43562800-43563200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:43562800-43563400	Weak transcription	NHDF-Ad	bronchial

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