Variant report

Variant	rs12023358
Chromosome Location	chr1:154399649-154399650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154377513..154380266-chr1:154397854..154400617,3	MCF-7	breast:
2	chr1:154390689..154395033-chr1:154398195..154400850,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10159236	0.83[EUR][1000 genomes]
rs11265618	0.81[ASN][1000 genomes]
rs11804305	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12047973	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12048091	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12048950	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4308966	0.83[EUR][1000 genomes]
rs4329505	0.83[EUR][1000 genomes]
rs4345796	0.81[EUR][1000 genomes]
rs4845626	0.82[ASN][1000 genomes]
rs55800510	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55826755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57502626	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61812592	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61812593	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61812594	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61812596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61812599	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61812626	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154383000-154402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154389000-154402800	Enhancers	Stomach Mucosa	stomach
3	chr1:154392800-154400200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr1:154392800-154400600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:154392800-154402800	Weak transcription	Fetal Brain Male	brain
6	chr1:154393000-154405800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr1:154393600-154402800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:154393800-154399800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:154393800-154401200	Enhancers	Hela-S3	cervix
10	chr1:154393800-154402600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:154393800-154403600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:154394000-154404000	Weak transcription	GM12878-XiMat	blood
13	chr1:154394200-154399800	Weak transcription	Ovary	ovary
14	chr1:154395600-154400200	Weak transcription	Fetal Thymus	thymus
15	chr1:154395600-154401200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:154396800-154399800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:154396800-154399800	Enhancers	Colon Smooth Muscle	Colon
18	chr1:154396800-154400000	Weak transcription	Fetal Brain Female	brain
19	chr1:154396800-154401200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:154396800-154401600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:154396800-154402200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:154397000-154399800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:154397000-154399800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:154397000-154399800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:154397000-154399800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:154397000-154399800	Weak transcription	Fetal Lung	lung
27	chr1:154397000-154399800	Weak transcription	Fetal Stomach	stomach
28	chr1:154397000-154399800	Weak transcription	Spleen	Spleen
29	chr1:154397000-154399800	Weak transcription	HSMMtube	muscle
30	chr1:154397000-154400000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:154397000-154400000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:154397000-154400000	Weak transcription	HSMM	muscle
33	chr1:154397000-154400200	Weak transcription	Fetal Kidney	kidney
34	chr1:154397000-154402200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:154397000-154402800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:154397000-154414200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:154397200-154399800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:154397200-154399800	Weak transcription	Brain Substantia Nigra	brain
39	chr1:154397200-154399800	Weak transcription	A549	lung
40	chr1:154397200-154399800	Weak transcription	Osteobl	bone
41	chr1:154397200-154400200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:154397200-154402400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:154397200-154402600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:154397200-154403800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:154397400-154399800	Weak transcription	Brain Anterior Caudate	brain
46	chr1:154397400-154399800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:154397400-154399800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:154397400-154399800	Weak transcription	NHDF-Ad	bronchial
49	chr1:154397400-154400000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:154397400-154400000	Weak transcription	Muscle Satellite Cultured Cells	--

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