Variant report

Variant	rs2488759
Chromosome Location	chr1:112942616-112942617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:112940392..112943025-chr1:112944284..112946532,3	K562	blood:
2	chr1:112935548..112944315-chr1:113002393..113010397,28	MCF-7	breast:
3	chr1:112940500..112942998-chr1:113216461..113219079,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134245	Chromatin interaction
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1018712	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1018713	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102471	0.83[EUR][1000 genomes]
rs11102472	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102475	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102477	0.91[ASN][1000 genomes]
rs11102479	0.90[ASN][1000 genomes]
rs1175629	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1177812	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1177813	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12119865	1.00[ASN][1000 genomes]
rs12126055	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1333231	0.96[ASN][1000 genomes]
rs1412931	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1475710	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1572048	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1759684	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1759688	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1759689	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1759692	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1777608	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1777615	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2026499	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2026500	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2026501	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2065543	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065544	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2184095	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2256883	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2483328	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483332	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2483333	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483338	0.82[ASN][1000 genomes]
rs2483339	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2483340	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483341	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483342	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483343	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483344	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483345	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483346	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483348	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2483349	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483350	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2483351	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2483352	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483356	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483357	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483358	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483359	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483360	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483361	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483362	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488757	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488758	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488761	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488762	0.81[EUR][1000 genomes]
rs2488786	0.84[ASN][1000 genomes]
rs2488787	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2488788	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2488789	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2488790	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2488791	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488792	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492506	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492507	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492509	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492510	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492511	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492512	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492513	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492514	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492515	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2492516	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492517	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492518	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492519	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492521	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492522	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492523	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492524	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492525	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492529	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492530	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492531	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492532	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492533	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2492534	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2780271	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2990988	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2990989	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999476	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122287	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762332	0.92[ASN][1000 genomes]
rs3762333	0.90[ASN][1000 genomes]
rs3795821	0.92[ASN][1000 genomes]
rs3818729	0.93[ASN][1000 genomes]
rs4240533	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4596887	0.93[ASN][1000 genomes]
rs4839245	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4839246	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55835005	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56303798	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666369	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6680402	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695156	0.89[ASN][1000 genomes]
rs6696624	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703430	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536263	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7541222	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962401	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2488759	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112939800-112944200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:112939800-112944600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:112940000-112943800	Weak transcription	Brain Substantia Nigra	brain
4	chr1:112940000-112944000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:112940000-112944200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:112940000-112944600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:112940000-112945800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:112940000-112950600	Weak transcription	Lung	lung
9	chr1:112940000-112952200	Weak transcription	Esophagus	oesophagus
10	chr1:112940000-112954400	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:112940000-112956400	Weak transcription	Left Ventricle	heart
12	chr1:112940000-112961400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:112940200-112943600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:112940200-112958400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:112940400-112944200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:112940400-112944200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:112940600-112942800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:112940600-112943800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:112940600-112943800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:112940600-112945200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:112940600-112945400	Weak transcription	Fetal Heart	heart
22	chr1:112940600-112945800	Weak transcription	Ovary	ovary
23	chr1:112940600-112958800	Weak transcription	Colonic Mucosa	Colon
24	chr1:112940600-112962000	Weak transcription	Psoas Muscle	Psoas
25	chr1:112940800-112942800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:112940800-112943800	Weak transcription	Brain Angular Gyrus	brain
27	chr1:112940800-112943800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:112940800-112944200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:112940800-112946000	Weak transcription	HepG2	liver
30	chr1:112940800-112946800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:112940800-112955000	Weak transcription	Adipose Nuclei	Adipose
32	chr1:112941000-112942800	Weak transcription	NHDF-Ad	bronchial
33	chr1:112941000-112943000	Enhancers	Fetal Brain Male	brain
34	chr1:112941000-112943800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:112941000-112943800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:112941000-112943800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:112941000-112943800	Weak transcription	A549	lung
38	chr1:112941000-112944600	Weak transcription	HMEC	breast
39	chr1:112941000-112946400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:112941000-112946400	Weak transcription	Aorta	Aorta
41	chr1:112941000-112949000	Weak transcription	Fetal Lung	lung
42	chr1:112941000-112949000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:112941200-112942800	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:112941200-112942800	Weak transcription	NHLF	lung
45	chr1:112941200-112943000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:112941200-112943600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:112941200-112943600	Weak transcription	Osteobl	bone
48	chr1:112941200-112943800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:112941200-112943800	Weak transcription	Hela-S3	cervix
50	chr1:112941200-112943800	Weak transcription	NH-A	brain

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