Variant report

Variant	rs12028246
Chromosome Location	chr1:166831133-166831134
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:166817024..166819556-chr1:166829246..166831714,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10800267	0.83[ASN][1000 genomes]
rs10800268	0.91[ASN][1000 genomes]
rs10800269	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10800271	0.83[ASN][1000 genomes]
rs10800273	0.81[ASN][1000 genomes]
rs10918586	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10918587	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12029327	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12029367	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12032642	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12039764	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12117020	0.85[EUR][1000 genomes]
rs12122547	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476348	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476349	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476350	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17331024	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075947	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232521	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272793	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35622400	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738209	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753910	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4657607	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61408535	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427038	0.81[ASN][1000 genomes]
rs6675033	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675153	0.96[ASN][1000 genomes]
rs6675750	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6677387	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6691431	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6718	0.97[ASN][1000 genomes]
rs742006	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7531189	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs760537	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12028246	DUTP6	cis	Esophagus Muscularis	GTEx
rs12028246	MAEL	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166809600-166844400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:166810600-166834800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:166810600-166838800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:166810800-166832400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:166810800-166834200	Strong transcription	Fetal Stomach	stomach
6	chr1:166810800-166835200	Strong transcription	K562	blood
7	chr1:166810800-166839200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:166810800-166839200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:166811000-166835600	Strong transcription	Primary B cells from cord blood	blood
10	chr1:166811200-166834600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:166811200-166839800	Strong transcription	Primary T cells from cord blood	blood
12	chr1:166811800-166838600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:166811800-166838600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:166812000-166838400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:166812000-166838800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:166812200-166838800	Strong transcription	Fetal Thymus	thymus
17	chr1:166813000-166834200	Strong transcription	Hela-S3	cervix
18	chr1:166813200-166832000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr1:166813200-166834600	Strong transcription	Placenta	Placenta
20	chr1:166813200-166840600	Strong transcription	Dnd41	blood
21	chr1:166813400-166838400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:166813600-166838600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:166813600-166839200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr1:166813800-166838400	Strong transcription	Fetal Intestine Large	intestine
25	chr1:166814200-166834000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:166814200-166834600	Strong transcription	Adipose Nuclei	Adipose
27	chr1:166814200-166838800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:166814400-166831600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:166814400-166833800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:166814400-166834200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr1:166814400-166834400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr1:166814400-166835800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr1:166814600-166834200	Strong transcription	Osteobl	bone
34	chr1:166814800-166834600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:166814800-166838200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:166815000-166833800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:166815200-166838400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr1:166815400-166838200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:166819400-166841400	Weak transcription	Stomach Mucosa	stomach
40	chr1:166819600-166838400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr1:166819800-166842600	Weak transcription	Small Intestine	intestine
42	chr1:166821200-166835800	Strong transcription	Fetal Brain Female	brain
43	chr1:166823000-166834000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:166823200-166834200	Strong transcription	Thymus	Thymus
45	chr1:166824400-166837200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:166824600-166838200	Strong transcription	Fetal Intestine Small	intestine
47	chr1:166825000-166834200	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:166825000-166844400	Weak transcription	HSMMtube	muscle
49	chr1:166825200-166832600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:166825600-166839200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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