Variant report

Variant	rs12402134
Chromosome Location	chr1:160078891-160078892
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	chr1:160077475..160080370-chr1:160230090..160233293,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132716	Chromatin interaction
ENSG00000228606	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11265317	0.86[AFR][1000 genomes]
rs11265328	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1131891	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12401984	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12402888	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12407381	0.84[AMR][1000 genomes]
rs12408200	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12408584	0.86[AFR][1000 genomes]
rs12410866	0.84[AMR][1000 genomes]
rs12727520	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17846705	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17846715	0.89[AMR][1000 genomes]
rs1884998	0.84[EUR][1000 genomes]
rs3747619	0.81[CEU][hapmap]
rs3761684	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41265757	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4656879	0.96[ASN][1000 genomes]
rs55753565	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56187338	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs56211999	0.86[AFR][1000 genomes]
rs56287743	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61822013	0.86[AFR][1000 genomes]
rs61822015	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv520189	chr1:160011512-160095625	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1806746	chr1:160029416-160105927	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824420	chr1:160029416-160105927	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1843994	chr1:160029416-160105927	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv534066	chr1:160029416-160105986	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv1794281	chr1:160029416-160111565	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv1820784	chr1:160029416-160159395	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv534165	chr1:160029416-160187302	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160072800-160083200	Weak transcription	Right Atrium	heart
2	chr1:160074000-160079000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:160074200-160081800	Weak transcription	Right Ventricle	heart
4	chr1:160074400-160083200	Weak transcription	Aorta	Aorta
5	chr1:160074600-160079000	Weak transcription	Brain Germinal Matrix	brain
6	chr1:160074800-160079000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:160074800-160079000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:160074800-160079200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:160074800-160082400	Weak transcription	Colonic Mucosa	Colon
10	chr1:160074800-160083400	Weak transcription	HSMMtube	muscle
11	chr1:160074800-160086400	Weak transcription	Spleen	Spleen
12	chr1:160075000-160083400	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:160075400-160079800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:160075600-160082200	Weak transcription	Brain Angular Gyrus	brain
15	chr1:160077200-160082400	Weak transcription	Brain Substantia Nigra	brain
16	chr1:160077400-160080800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:160077800-160079000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:160078200-160079800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:160078200-160079800	Enhancers	Brain Hippocampus Middle	brain
20	chr1:160078200-160080600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr1:160078400-160079200	Enhancers	Placenta	Placenta
22	chr1:160078400-160079200	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr1:160078400-160079400	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:160078400-160079400	Enhancers	Lung	lung
25	chr1:160078400-160079600	Enhancers	Brain Anterior Caudate	brain
26	chr1:160078400-160079800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:160078400-160079800	Enhancers	Ovary	ovary
28	chr1:160078400-160079800	Enhancers	A549	lung
29	chr1:160078400-160080200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:160078400-160080400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:160078400-160080400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:160078400-160080400	Enhancers	H9 Cell Line	embryonic stem cell
33	chr1:160078400-160080400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr1:160078400-160080400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:160078400-160080400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:160078400-160080400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:160078400-160080400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:160078400-160080600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:160078400-160080600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr1:160078400-160080600	Enhancers	Fetal Muscle Trunk	muscle
41	chr1:160078400-160080800	Enhancers	H1 Cell Line	embryonic stem cell
42	chr1:160078400-160085400	Enhancers	Fetal Muscle Leg	muscle
43	chr1:160078600-160079000	Weak transcription	Left Ventricle	heart
44	chr1:160078600-160079200	Enhancers	Hela-S3	cervix
45	chr1:160078600-160079400	Enhancers	Fetal Heart	heart
46	chr1:160078600-160079600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr1:160078600-160079600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:160078600-160079600	Enhancers	HSMM	muscle
49	chr1:160078600-160079800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:160078600-160080200	Enhancers	HUES64 Cell Line	embryonic stem cell

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