Variant report

Variant	rs2488757
Chromosome Location	chr1:112946903-112946904
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	chr1:112945712..112947668-chr1:112948180..112951090,2	MCF-7	breast:

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1018712	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1018713	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102471	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs11102472	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102475	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102477	0.91[ASN][1000 genomes]
rs11102479	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1175629	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1177812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1177813	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12119865	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12126055	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1333231	0.96[ASN][1000 genomes]
rs1412931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1419041	0.82[CEU][hapmap]
rs1475710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1572048	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1759684	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1759688	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1759689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1759692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1777608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1777615	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1891705	0.82[CEU][hapmap]
rs2026499	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2026500	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2026501	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2065543	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065544	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2184095	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2256883	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2483328	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483332	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2483333	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483338	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2483339	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2483340	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483341	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483342	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483343	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483344	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483345	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2483346	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483348	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2483349	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483350	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2483351	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2483352	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483356	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483357	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483358	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483359	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483360	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483361	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483362	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488759	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488761	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488762	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2488768	0.83[CEU][hapmap]
rs2488769	0.82[CEU][hapmap]
rs2488786	0.91[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2488787	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2488788	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2488789	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2488790	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2488791	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2488792	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492502	0.82[CEU][hapmap]
rs2492506	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492509	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492510	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2492511	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492514	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492515	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2492516	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492517	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492518	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492519	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492521	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492522	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492523	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492524	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492525	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492529	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492530	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492531	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492532	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2492533	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2492534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2780271	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2990988	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2990989	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999472	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs2999476	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3122287	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762332	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs3762333	0.90[ASN][1000 genomes]
rs3795821	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs3818729	0.93[ASN][1000 genomes]
rs4240533	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4596887	0.93[ASN][1000 genomes]
rs4839245	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4839246	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55835005	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56303798	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6666369	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6680402	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695156	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6696624	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703430	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536263	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7541222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962401	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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
5	esv1850997	chr1:112944472-112993754	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2488757	CTTNBP2NL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:112940000-112950600	Weak transcription	Lung	lung
2	chr1:112940000-112952200	Weak transcription	Esophagus	oesophagus
3	chr1:112940000-112954400	Weak transcription	Fetal Muscle Leg	muscle
4	chr1:112940000-112956400	Weak transcription	Left Ventricle	heart
5	chr1:112940000-112961400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:112940200-112958400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:112940600-112958800	Weak transcription	Colonic Mucosa	Colon
8	chr1:112940600-112962000	Weak transcription	Psoas Muscle	Psoas
9	chr1:112940800-112955000	Weak transcription	Adipose Nuclei	Adipose
10	chr1:112941000-112949000	Weak transcription	Fetal Lung	lung
11	chr1:112941000-112949000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:112941200-112949200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:112941200-112955000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:112941200-112955000	Weak transcription	Fetal Kidney	kidney
15	chr1:112941400-112954400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:112941400-112956400	Weak transcription	Fetal Intestine Small	intestine
17	chr1:112941400-112959400	Weak transcription	Brain Germinal Matrix	brain
18	chr1:112941600-112959600	Weak transcription	Fetal Brain Female	brain
19	chr1:112942400-112952200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:112942400-112988200	Weak transcription	Small Intestine	intestine
21	chr1:112942600-112947000	Weak transcription	Right Atrium	heart
22	chr1:112942600-112954800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:112942600-112955400	Weak transcription	Fetal Intestine Large	intestine
24	chr1:112942600-112966400	Weak transcription	Spleen	Spleen
25	chr1:112942600-112967000	Weak transcription	Pancreas	Pancrea
26	chr1:112943000-112947000	Weak transcription	Stomach Mucosa	stomach
27	chr1:112943400-112949200	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr1:112943400-112950400	Enhancers	NHDF-Ad	bronchial
29	chr1:112943800-112947400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:112943800-112947600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:112944000-112947400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:112944200-112947400	Enhancers	H1 Cell Line	embryonic stem cell
33	chr1:112944200-112948000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:112944600-112947000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:112944600-112947200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:112944600-112949000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:112944800-112947600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:112944800-112959000	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:112945000-112947400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:112945000-112966400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:112945200-112947400	Enhancers	Colon Smooth Muscle	Colon
42	chr1:112945200-112949800	Weak transcription	Fetal Brain Male	brain
43	chr1:112945400-112947200	Genic enhancers	Rectal Mucosa Donor 31	rectum
44	chr1:112945400-112947800	Enhancers	Fetal Heart	heart
45	chr1:112945600-112947400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:112945600-112948800	Weak transcription	Brain Angular Gyrus	brain
47	chr1:112945800-112947000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:112945800-112947000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr1:112945800-112947000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr1:112945800-112947200	Enhancers	Ovary	ovary

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