Variant report

Variant	rs12401984
Chromosome Location	chr1:160077169-160077170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11265317	0.86[AFR][1000 genomes]
rs11265328	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1131891	0.93[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12092798	0.81[CEU][hapmap]
rs12401728	0.81[CEU][hapmap]
rs12402134	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12402888	0.93[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12408242	0.81[CEU][hapmap]
rs12408584	0.86[AFR][1000 genomes]
rs12410866	0.82[JPT][hapmap]
rs12727520	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17846705	0.83[AFR][1000 genomes]
rs1884998	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3747619	0.93[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs3761684	0.86[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs41265757	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4656879	1.00[JPT][hapmap]
rs55753565	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56187338	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56211999	0.86[AFR][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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160071200-160077600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:160071400-160078400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:160072600-160078600	Weak transcription	Fetal Heart	heart
4	chr1:160072800-160078400	Weak transcription	Lung	lung
5	chr1:160072800-160083200	Weak transcription	Right Atrium	heart
6	chr1:160073000-160078400	Weak transcription	Left Ventricle	heart
7	chr1:160073200-160078400	Weak transcription	A549	lung
8	chr1:160073200-160078600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:160073200-160078800	Weak transcription	Adipose Nuclei	Adipose
10	chr1:160073400-160078800	Weak transcription	Fetal Kidney	kidney
11	chr1:160074000-160079000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:160074200-160078400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:160074200-160078600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:160074200-160081800	Weak transcription	Right Ventricle	heart
15	chr1:160074400-160078400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:160074400-160078400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:160074400-160078400	Weak transcription	Ovary	ovary
18	chr1:160074400-160078600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:160074400-160078800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:160074400-160083200	Weak transcription	Aorta	Aorta
21	chr1:160074600-160078200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:160074600-160078400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:160074600-160078600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:160074600-160078600	Weak transcription	HSMM	muscle
25	chr1:160074600-160078800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:160074600-160079000	Weak transcription	Brain Germinal Matrix	brain
27	chr1:160074800-160077600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:160074800-160078200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:160074800-160078400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:160074800-160078400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:160074800-160078400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:160074800-160078400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:160074800-160078600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:160074800-160078800	Weak transcription	Fetal Lung	lung
35	chr1:160074800-160078800	Weak transcription	Fetal Stomach	stomach
36	chr1:160074800-160078800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:160074800-160079000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:160074800-160079000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:160074800-160079200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:160074800-160082400	Weak transcription	Colonic Mucosa	Colon
41	chr1:160074800-160083400	Weak transcription	HSMMtube	muscle
42	chr1:160074800-160086400	Weak transcription	Spleen	Spleen
43	chr1:160075000-160077600	Weak transcription	HepG2	liver
44	chr1:160075000-160083400	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:160075400-160078400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:160075400-160078400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:160075400-160079800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:160075600-160077600	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:160075600-160078400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:160075600-160078400	Weak transcription	Brain Cingulate Gyrus	brain

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