Variant report

Variant	rs12024140
Chromosome Location	chr1:57039895-57039896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12024524	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12088488	0.88[CEU][hapmap]
rs1777283	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4475779	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6675286	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539051	0.81[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57017800-57040800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr1:57025600-57040000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:57029400-57042200	Weak transcription	Thymus	Thymus
4	chr1:57032200-57040600	Weak transcription	HSMM	muscle
5	chr1:57032400-57042400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:57032800-57041000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:57035200-57041400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:57036400-57040800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:57036600-57040600	Enhancers	Brain Cingulate Gyrus	brain
10	chr1:57036600-57040600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr1:57036800-57041600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:57037000-57040000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr1:57037200-57040000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:57037200-57040400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:57037200-57042400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:57037200-57042400	Weak transcription	Gastric	stomach
17	chr1:57038000-57043400	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr1:57038000-57043800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:57038200-57040200	Enhancers	Fetal Lung	lung
20	chr1:57038200-57041000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
21	chr1:57038200-57042400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:57038200-57042400	Weak transcription	Esophagus	oesophagus
23	chr1:57038400-57043200	Weak transcription	Spleen	Spleen
24	chr1:57038800-57040000	Enhancers	Brain Hippocampus Middle	brain
25	chr1:57038800-57040200	Weak transcription	Right Ventricle	heart
26	chr1:57039000-57040000	Flanking Active TSS	Ovary	ovary
27	chr1:57039000-57040000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:57039000-57040200	Weak transcription	Primary B cells from cord blood	blood
29	chr1:57039000-57040200	Weak transcription	A549	lung
30	chr1:57039000-57040800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:57039000-57040800	Enhancers	HUVEC	blood vessel
32	chr1:57039000-57041400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:57039000-57042000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:57039000-57042400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:57039000-57042600	Active TSS	Psoas Muscle	Psoas
36	chr1:57039200-57040400	Weak transcription	Brain Germinal Matrix	brain
37	chr1:57039200-57041200	Weak transcription	Aorta	Aorta
38	chr1:57039200-57041600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:57039200-57042400	Active TSS	Stomach Smooth Muscle	stomach
40	chr1:57039400-57040000	Weak transcription	Fetal Brain Female	brain
41	chr1:57039400-57040000	Weak transcription	Fetal Kidney	kidney
42	chr1:57039400-57040200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:57039400-57040200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:57039400-57040200	Flanking Active TSS	Placenta	Placenta
45	chr1:57039400-57040400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:57039400-57040400	Enhancers	Pancreas	Pancrea
47	chr1:57039400-57040600	Active TSS	Brain Anterior Caudate	brain
48	chr1:57039400-57040600	Weak transcription	Fetal Intestine Small	intestine
49	chr1:57039400-57040600	Weak transcription	Fetal Stomach	stomach
50	chr1:57039400-57040800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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