Variant report

Variant	rs232826
Chromosome Location	chr1:59047932-59047933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:59047843..59052771-chr1:59082760..59087529,8	MCF-7	breast:
2	chr1:59046705..59048378-chr1:59112246..59114318,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10458559	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10789064	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10789065	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10789066	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10789067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10889098	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs10889100	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10889101	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1109895	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1109896	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11207237	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs11207250	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11207251	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11207252	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11207253	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11207254	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11581395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs12030713	0.95[CEU][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12124662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs12125391	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12142098	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1388981	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1775002	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2087799	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs232822	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232827	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232830	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs232841	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs232842	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs232844	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs232847	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs232848	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs232849	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2406784	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3087585	0.95[CEU][hapmap]
rs338225	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs3551	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4912195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4912344	0.82[ASN][1000 genomes]
rs525929	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs562166	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs584579	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs602579	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs603031	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61779295	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61779296	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs620342	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs627218	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6587819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6587820	0.91[CEU][hapmap]
rs6587828	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs659061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6656025	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6667614	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs6667703	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs6687324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs672359	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67639631	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7355165	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7355166	0.82[EUR][1000 genomes]
rs7517424	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7520008	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7536230	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7544032	0.82[ASN][1000 genomes]
rs7546900	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7547036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs905567	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9660901	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs232826	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL
rs232826	TACSTD2	cis	Whole Blood	GTEx
rs232826	TACSTD2	cis	Thyroid	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59043200-59049200	Weak transcription	Gastric	stomach
2	chr1:59043400-59049000	Weak transcription	Pancreas	Pancrea
3	chr1:59043400-59049800	Weak transcription	Ovary	ovary
4	chr1:59043600-59049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:59043800-59049000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:59043800-59049000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:59043800-59049200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:59043800-59049200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:59044000-59049000	Weak transcription	Fetal Lung	lung
10	chr1:59044000-59049000	Weak transcription	Osteobl	bone
11	chr1:59044000-59049200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:59044000-59049200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:59044000-59049400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:59044000-59049800	Weak transcription	Brain Angular Gyrus	brain
15	chr1:59044200-59049000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:59044200-59049000	Weak transcription	Spleen	Spleen
17	chr1:59044200-59049200	Weak transcription	Adipose Nuclei	Adipose
18	chr1:59044400-59049000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:59044400-59049000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:59044400-59049000	Weak transcription	Stomach Mucosa	stomach
21	chr1:59045400-59049000	Weak transcription	Hela-S3	cervix
22	chr1:59045400-59049000	Weak transcription	HMEC	breast
23	chr1:59046000-59049000	Weak transcription	Lung	lung
24	chr1:59046200-59049000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:59046200-59049000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:59046200-59049000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:59046200-59049000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:59046200-59049000	Weak transcription	Placenta	Placenta
29	chr1:59046200-59049000	Weak transcription	NHEK	skin
30	chr1:59047000-59049000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr1:59047800-59049000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:59047800-59049000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:59047800-59049000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:59047800-59049000	Weak transcription	HSMM	muscle
35	chr1:59047800-59049000	Weak transcription	HSMMtube	muscle
36	chr1:59047800-59049000	Weak transcription	HUVEC	blood vessel

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