Variant report

Variant	rs2132001
Chromosome Location	chr5:43472984-43472985
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	chr5:43469236..43473884-chr5:43482769..43486101,7	MCF-7	breast:
2	chr5:43402066..43404544-chr5:43469955..43473241,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151881	Chromatin interaction
ENSG00000249492	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10036954	0.88[ASN][1000 genomes]
rs10038545	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10053229	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10054519	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10059912	0.81[ASN][1000 genomes]
rs10066408	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10068064	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10074682	0.84[ASN][1000 genomes]
rs10472380	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10473310	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10473311	0.92[ASN][1000 genomes]
rs1389868	0.82[ASN][1000 genomes]
rs1389869	0.88[ASN][1000 genomes]
rs1389870	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1593971	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2131998	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2132003	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28437972	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3776423	0.88[ASN][1000 genomes]
rs4072918	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4072919	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4074777	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4331909	0.81[ASN][1000 genomes]
rs4467713	0.81[ASN][1000 genomes]
rs4866831	0.82[ASN][1000 genomes]
rs4866833	0.81[ASN][1000 genomes]
rs4866835	0.81[ASN][1000 genomes]
rs55855322	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56333629	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57403343	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57547662	0.88[ASN][1000 genomes]
rs59001943	0.81[ASN][1000 genomes]
rs60297702	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6451695	0.88[ASN][1000 genomes]
rs6451696	0.88[ASN][1000 genomes]
rs6451697	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6451699	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6451704	0.96[ASN][1000 genomes]
rs6451705	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6451712	0.81[ASN][1000 genomes]
rs66495712	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67466542	0.88[ASN][1000 genomes]
rs6858942	0.96[ASN][1000 genomes]
rs6862102	0.86[ASN][1000 genomes]
rs6866325	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6866802	0.81[ASN][1000 genomes]
rs6869933	0.81[ASN][1000 genomes]
rs6870018	0.88[ASN][1000 genomes]
rs6878770	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6884661	0.81[ASN][1000 genomes]
rs6885679	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6891363	0.81[ASN][1000 genomes]
rs6895327	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6896693	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72756535	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73100614	0.83[ASN][1000 genomes]
rs750583	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7710628	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7718627	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7732140	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7736108	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2132001	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43433800-43483400	Weak transcription	Gastric	stomach
2	chr5:43444000-43482600	Weak transcription	HMEC	breast
3	chr5:43444800-43482600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:43453800-43482600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:43454000-43482400	Weak transcription	Osteobl	bone
6	chr5:43454800-43482800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:43461000-43482400	Weak transcription	NHLF	lung
8	chr5:43461200-43482800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:43461200-43483400	Weak transcription	Pancreas	Pancrea
10	chr5:43462200-43474000	Weak transcription	Lung	lung
11	chr5:43462200-43482600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:43462200-43482600	Weak transcription	Fetal Stomach	stomach
13	chr5:43462200-43482800	Weak transcription	Right Ventricle	heart
14	chr5:43462400-43483000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:43462400-43483400	Weak transcription	Spleen	Spleen
16	chr5:43464200-43480000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:43465600-43481200	Weak transcription	HepG2	liver
18	chr5:43467000-43482000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr5:43467000-43482800	Weak transcription	Primary T cells from cord blood	blood
20	chr5:43467200-43482800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:43467600-43482400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr5:43467800-43479800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:43467800-43482400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr5:43468000-43475800	Weak transcription	Hela-S3	cervix
25	chr5:43468000-43476000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:43468000-43476000	Weak transcription	NHEK	skin
27	chr5:43468000-43480200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:43468000-43480200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:43468000-43482400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr5:43468000-43482600	Weak transcription	Adipose Nuclei	Adipose
31	chr5:43468000-43482800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr5:43468200-43482400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:43468200-43482600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr5:43468200-43482600	Weak transcription	Liver	Liver
35	chr5:43468200-43482600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:43468200-43482800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:43468200-43482800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr5:43468200-43482800	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:43468200-43482800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr5:43468200-43482800	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:43468200-43482800	Weak transcription	Fetal Thymus	thymus
42	chr5:43468200-43482800	Weak transcription	Thymus	Thymus
43	chr5:43468200-43483200	Weak transcription	Aorta	Aorta
44	chr5:43468600-43482400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:43468800-43482800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr5:43468800-43483400	Weak transcription	Ovary	ovary
47	chr5:43469200-43482400	Weak transcription	Fetal Lung	lung
48	chr5:43470200-43481800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:43470200-43482200	Weak transcription	HSMMtube	muscle
50	chr5:43470200-43483000	Weak transcription	Fetal Intestine Small	intestine

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