Variant report

Variant	rs12059178
Chromosome Location	chr1:228872502-228872503
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228871721..228874007-chr1:228877352..228880161,2	MCF-7	breast:
2	chr1:228870974..228874192-chr1:229289899..229293413,3	MCF-7	breast:
3	chr1:228872086..228874934-chr1:228877939..228879672,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1006797	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10489542	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1108502	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12070785	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12075157	0.85[ASN][1000 genomes]
rs12076649	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12077418	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12078927	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12092986	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12096381	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535129	0.97[EUR][1000 genomes]
rs2009564	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2180162	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207704	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295255	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34036301	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4654625	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6667385	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681268	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7532644	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554565	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv468316	chr1:228854703-228919202	Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv549300	chr1:228854703-228919202	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv3405929	chr1:228869854-228872702	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228870200-228875400	Active TSS	Brain Angular Gyrus	brain
2	chr1:228870400-228872800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:228870400-228873200	Active TSS	Fetal Intestine Small	intestine
4	chr1:228870400-228873400	Active TSS	Fetal Intestine Large	intestine
5	chr1:228870400-228873800	Active TSS	Aorta	Aorta
6	chr1:228870400-228873800	Active TSS	Colonic Mucosa	Colon
7	chr1:228870400-228873800	Active TSS	Right Ventricle	heart
8	chr1:228870400-228874000	Active TSS	Brain Anterior Caudate	brain
9	chr1:228870400-228874200	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr1:228870600-228872600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
11	chr1:228870600-228872600	Active TSS	Primary T cells from cord blood	blood
12	chr1:228870600-228872800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:228870600-228873000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:228870600-228873000	Active TSS	Colon Smooth Muscle	Colon
15	chr1:228870600-228873000	Active TSS	A549	lung
16	chr1:228870600-228873200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:228870600-228873200	Active TSS	Liver	Liver
18	chr1:228870600-228873200	Active TSS	Ovary	ovary
19	chr1:228870600-228873400	Active TSS	Pancreas	Pancrea
20	chr1:228870600-228873400	Active TSS	Placenta Amnion	Placenta Amnion
21	chr1:228870600-228873400	Active TSS	Psoas Muscle	Psoas
22	chr1:228870600-228873600	Active TSS	Brain Substantia Nigra	brain
23	chr1:228870600-228873600	Active TSS	Duodenum Mucosa	Duodenum
24	chr1:228870600-228873600	Active TSS	Fetal Lung	lung
25	chr1:228870600-228874000	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:228870600-228874000	Active TSS	Right Atrium	heart
27	chr1:228870600-228874200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:228870600-228874400	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr1:228870600-228875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:228870800-228872600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr1:228870800-228872800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr1:228870800-228872800	Active TSS	Stomach Smooth Muscle	stomach
33	chr1:228870800-228873000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:228870800-228873000	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr1:228870800-228873000	Active TSS	HepG2	liver
36	chr1:228870800-228873200	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr1:228870800-228873400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:228870800-228873400	Active TSS	Small Intestine	intestine
39	chr1:228870800-228873600	Active TSS	Brain Cingulate Gyrus	brain
40	chr1:228870800-228873600	Active TSS	Brain Hippocampus Middle	brain
41	chr1:228870800-228873600	Active TSS	Gastric	stomach
42	chr1:228870800-228873800	Active TSS	Rectal Smooth Muscle	rectum
43	chr1:228870800-228874000	Active TSS	Fetal Brain Female	brain
44	chr1:228871000-228872600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:228871000-228872600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:228871000-228872800	Active TSS	Placenta	Placenta
47	chr1:228871000-228873200	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr1:228871600-228872600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:228871600-228872600	Active TSS	Esophagus	oesophagus
50	chr1:228871600-228873000	Active TSS	Stomach Mucosa	stomach

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