Variant report

Variant	rs12027142
Chromosome Location	chr1:93728648-93728649
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93728185..93731169-chr1:93735951..93738017,2	MCF-7	breast:
2	chr1:93725585..93728395-chr1:93728407..93730397,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10874766	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164885	0.87[ASN][1000 genomes]
rs11164896	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11164897	0.81[ASN][1000 genomes]
rs11164905	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11164908	0.81[ASN][1000 genomes]
rs12030843	0.87[ASN][1000 genomes]
rs12031709	0.82[ASN][1000 genomes]
rs12031765	0.87[ASN][1000 genomes]
rs12033147	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12036057	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12038046	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12044557	0.87[ASN][1000 genomes]
rs12045001	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12046063	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048219	0.88[ASN][1000 genomes]
rs12405487	0.84[ASN][1000 genomes]
rs12563709	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566752	0.81[ASN][1000 genomes]
rs2255722	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2391251	0.84[ASN][1000 genomes]
rs2484486	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2783490	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2783493	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2783495	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2783496	0.92[EUR][1000 genomes]
rs2783497	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2783505	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815406	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28782525	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2893242	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087457	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3904665	0.87[ASN][1000 genomes]
rs3904666	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4484937	0.86[ASN][1000 genomes]
rs58354545	0.87[ASN][1000 genomes]
rs61266405	0.81[ASN][1000 genomes]
rs61799470	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61799497	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61799500	0.87[ASN][1000 genomes]
rs61799516	0.84[ASN][1000 genomes]
rs61799517	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61799538	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6676902	0.84[ASN][1000 genomes]
rs6684908	0.84[ASN][1000 genomes]
rs72959220	0.87[ASN][1000 genomes]
rs771454	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs771461	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs771465	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs771470	0.82[EUR][1000 genomes]
rs771476	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs771479	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs771482	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs810027	0.84[EUR][1000 genomes];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	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12027142	DR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93756400	Weak transcription	Gastric	stomach
2	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:93690400-93729400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:93691200-93732400	Weak transcription	HUVEC	blood vessel
5	chr1:93692200-93787800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:93704200-93729800	Weak transcription	Hela-S3	cervix
7	chr1:93720000-93762000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:93721200-93731400	Weak transcription	NH-A	brain
9	chr1:93724200-93731800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:93725200-93732600	Weak transcription	NHDF-Ad	bronchial
11	chr1:93726200-93729800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
12	chr1:93726400-93729800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:93726400-93730200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:93726400-93731600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:93726400-93731800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
16	chr1:93726400-93732000	Weak transcription	Right Ventricle	heart
17	chr1:93726600-93731800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
18	chr1:93726600-93731800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr1:93726800-93730000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr1:93726800-93730400	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr1:93726800-93731200	ZNF genes & repeats	GM12878-XiMat	blood
22	chr1:93726800-93731800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr1:93727000-93728800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:93727000-93728800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
25	chr1:93727000-93728800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
26	chr1:93727000-93728800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
27	chr1:93727000-93728800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:93727000-93728800	ZNF genes & repeats	Fetal Intestine Large	intestine
29	chr1:93727000-93728800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:93727000-93729000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
31	chr1:93727000-93729000	Strong transcription	Osteobl	bone
32	chr1:93727000-93729200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
33	chr1:93727000-93729200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
34	chr1:93727000-93729600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr1:93727000-93729800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
36	chr1:93727000-93729800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr1:93727000-93729800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:93727000-93730000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
39	chr1:93727000-93730400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
40	chr1:93727000-93730400	Strong transcription	Fetal Lung	lung
41	chr1:93727000-93731200	ZNF genes & repeats	Dnd41	blood
42	chr1:93727000-93731800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:93727200-93728800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:93727200-93729800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
45	chr1:93727400-93728800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
46	chr1:93727400-93728800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:93727400-93728800	ZNF genes & repeats	Liver	Liver
48	chr1:93727400-93728800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
49	chr1:93727400-93728800	ZNF genes & repeats	Spleen	Spleen
50	chr1:93727400-93729000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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