Variant report

Variant	rs12623408
Chromosome Location	chr2:233569951-233569952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233560777..233562416-chr2:233568775..233570422,2	K562	blood:

Variant related genes	Relation type
ENSG00000204120	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12619228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2241979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2289912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3816335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4973052	0.83[AMR][1000 genomes]
rs72617178	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72617179	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72617180	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72617181	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72617182	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72617183	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72617184	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233563200-233572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:233563800-233582600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:233564000-233570600	Weak transcription	Fetal Kidney	kidney
4	chr2:233564000-233570800	Weak transcription	HSMMtube	muscle
5	chr2:233564000-233579600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:233564000-233589000	Weak transcription	NH-A	brain
7	chr2:233564200-233570000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:233564200-233570400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:233564200-233571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:233564200-233596400	Weak transcription	NHLF	lung
11	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:233564800-233592800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
14	chr2:233565200-233573800	Weak transcription	NHEK	skin
15	chr2:233565200-233589800	Weak transcription	HMEC	breast
16	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
17	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
18	chr2:233565400-233580200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:233565400-233589800	Weak transcription	Hela-S3	cervix
20	chr2:233565400-233590000	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr2:233566000-233570400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:233566000-233576000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:233566000-233576000	Strong transcription	Fetal Stomach	stomach
25	chr2:233566000-233577000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:233566000-233578400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:233566000-233584600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:233566200-233574200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:233566200-233576000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:233566400-233572000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:233566600-233570600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr2:233566800-233571000	Weak transcription	Ovary	ovary
33	chr2:233566800-233571000	Weak transcription	Right Ventricle	heart
34	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
35	chr2:233567200-233574200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:233567200-233574200	Strong transcription	Fetal Thymus	thymus
37	chr2:233567400-233572200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:233567400-233576800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:233567600-233572200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr2:233567600-233572400	Strong transcription	GM12878-XiMat	blood
41	chr2:233567600-233577800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:233567800-233571400	Strong transcription	Left Ventricle	heart
43	chr2:233567800-233573800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:233567800-233574000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:233567800-233575800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:233568000-233572600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:233568000-233573400	Strong transcription	Dnd41	blood
48	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr2:233568200-233571000	Strong transcription	Fetal Brain Female	brain
50	chr2:233568200-233571200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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