Variant report

Variant	rs196123
Chromosome Location	chr2:63841712-63841713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:63839924..63841875-chr2:64097480..64100299,2	MCF-7	breast:
2	chr2:63838300..63840634-chr2:63841674..63843707,2	K562	blood:
3	chr2:63835075..63837932-chr2:63839225..63843249,3	K562	blood:
4	chr2:63823578..63825836-chr2:63839966..63841886,2	K562	blood:
5	chr2:63814966..63816928-chr2:63840140..63842095,2	MCF-7	breast:
6	chr2:63840506..63842686-chr2:63842776..63844510,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143951	Chromatin interaction
ENSG00000014641	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs10168545	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1023820	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10469944	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10469945	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082363	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865337	0.89[ASN][1000 genomes]
rs10865338	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865339	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125977	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11125978	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs112194	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693909	0.89[ASN][1000 genomes]
rs11898615	0.82[EUR][1000 genomes]
rs12105140	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1255	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713496	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12990914	0.83[EUR][1000 genomes]
rs1348803	0.90[ASN][1000 genomes]
rs1348806	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1374308	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1446563	0.90[ASN][1000 genomes]
rs1446564	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1446565	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1446569	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550860	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs166384	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166385	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs171901	0.90[ASN][1000 genomes]
rs171902	0.90[ASN][1000 genomes]
rs174485	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs185499	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867847	0.81[EUR][1000 genomes]
rs1867849	0.82[EUR][1000 genomes]
rs187801	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900303	0.90[ASN][1000 genomes]
rs190519	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs196124	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs196125	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028883	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2028887	0.89[ASN][1000 genomes]
rs2121350	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2121351	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121353	0.90[ASN][1000 genomes]
rs2166494	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2166497	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305157	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422011	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2592386	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2592387	0.90[ASN][1000 genomes]
rs2592388	0.90[ASN][1000 genomes]
rs2604613	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2604614	0.90[ASN][1000 genomes]
rs2604615	0.90[ASN][1000 genomes]
rs262470	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262471	0.81[EUR][1000 genomes]
rs262472	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262473	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262474	0.81[EUR][1000 genomes]
rs262475	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262476	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262477	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262478	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262479	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs262480	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262481	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262482	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262483	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262484	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262485	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262487	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262488	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262490	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262491	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262492	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262493	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262494	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262495	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262501	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262502	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262503	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262504	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262505	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262506	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs262507	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs262508	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs262509	0.90[ASN][1000 genomes]
rs262510	0.82[AMR][1000 genomes]
rs262511	0.90[ASN][1000 genomes]
rs262512	0.90[ASN][1000 genomes]
rs262514	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs262515	0.90[ASN][1000 genomes]
rs262516	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs262517	0.90[ASN][1000 genomes]
rs262518	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs262519	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs262520	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs262521	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs262523	0.90[ASN][1000 genomes]
rs262524	0.82[AMR][1000 genomes]
rs262525	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs262526	0.90[ASN][1000 genomes]
rs262527	0.90[ASN][1000 genomes]
rs262528	0.90[ASN][1000 genomes]
rs262529	0.90[ASN][1000 genomes]
rs262530	0.90[ASN][1000 genomes]
rs262531	0.90[ASN][1000 genomes]
rs262533	0.90[ASN][1000 genomes]
rs262534	0.90[ASN][1000 genomes]
rs262535	0.90[ASN][1000 genomes]
rs262536	0.90[ASN][1000 genomes]
rs262537	0.90[ASN][1000 genomes]
rs262538	0.90[ASN][1000 genomes]
rs262539	0.90[ASN][1000 genomes]
rs2901614	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671065	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671067	0.89[ASN][1000 genomes]
rs4671068	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671069	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671515	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671516	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4671519	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6546007	0.82[EUR][1000 genomes]
rs6546009	0.82[EUR][1000 genomes]
rs6546017	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6546018	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546019	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706123	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6708804	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717031	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6724160	0.89[ASN][1000 genomes]
rs6732791	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6734648	0.83[EUR][1000 genomes]
rs6736029	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6738190	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68183503	0.81[EUR][1000 genomes]
rs7563623	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7570031	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7571017	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7571325	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7576316	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7577952	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7584404	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7606045	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607257	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs959195	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs964880	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964903	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9789351	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs989527	0.82[EUR][1000 genomes];0.89[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	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv1792289	chr2:63812148-63900292	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS 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	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs196123	WDPCP	cis	Adipose Subcutaneous	GTEx
rs196123	MDH1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63821600-63843000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:63833600-63841800	Weak transcription	K562	blood
3	chr2:63834200-63842400	Weak transcription	A549	lung
4	chr2:63834400-63841800	Weak transcription	HSMMtube	muscle
5	chr2:63834800-63842200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:63834800-63842400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:63834800-63842600	Weak transcription	Left Ventricle	heart
8	chr2:63835000-63842200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:63839600-63843400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr2:63839800-63842400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:63840000-63843000	Enhancers	Placenta	Placenta
12	chr2:63840000-63843600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:63840000-63844000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr2:63840200-63842400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:63840200-63843000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr2:63840200-63843800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:63840200-63844600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr2:63840400-63841800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr2:63840400-63842200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:63840400-63842400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:63840600-63842200	Enhancers	HMEC	breast
22	chr2:63840600-63842400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:63840600-63843000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:63840600-63844400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr2:63840800-63842400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:63840800-63842600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:63840800-63842800	Weak transcription	Psoas Muscle	Psoas
28	chr2:63840800-63844600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:63841000-63841800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:63841000-63842000	Enhancers	HepG2	liver
31	chr2:63841000-63843000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:63841000-63843000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:63841200-63842400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr2:63841200-63842400	Enhancers	HSMM	muscle
35	chr2:63841200-63842600	Enhancers	Osteobl	bone
36	chr2:63841400-63841800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr2:63841400-63841800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
38	chr2:63841400-63841800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:63841400-63841800	Flanking Active TSS	NH-A	brain
40	chr2:63841400-63842000	Enhancers	NHDF-Ad	bronchial
41	chr2:63841400-63842400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:63841400-63842600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:63841400-63842800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr2:63841600-63841800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:63841600-63841800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:63841600-63841800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:63841600-63842000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:63841600-63842000	Weak transcription	Adipose Nuclei	Adipose
49	chr2:63841600-63842200	Enhancers	Hela-S3	cervix
50	chr2:63841600-63842800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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