Variant report

Variant	rs12022839
Chromosome Location	chr1:58089133-58089134
allele	A/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:26)

rs_ID	r²[population]
rs10789051	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10889058	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207076	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207077	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207079	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207081	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11578358	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11588804	0.91[CHB][hapmap]
rs12029004	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12036858	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12038397	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12045520	0.80[CHB][hapmap]
rs12046948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12079319	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12085345	0.90[CHB][hapmap]
rs12755476	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1404384	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1524707	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1524708	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1539053	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1983454	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4912271	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57982718	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7544337	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7548317	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7548624	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]

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	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv871684	chr1:58021206-58096379	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58066400-58089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:58081200-58090600	Enhancers	Fetal Heart	heart
3	chr1:58081600-58089800	Enhancers	Fetal Muscle Leg	muscle
4	chr1:58085400-58093600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:58086200-58089800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:58086400-58089600	Enhancers	Fetal Brain Male	brain
7	chr1:58087800-58091600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr1:58088200-58089200	Enhancers	Fetal Kidney	kidney
9	chr1:58088200-58089400	Enhancers	Brain Hippocampus Middle	brain
10	chr1:58088200-58090400	Enhancers	Fetal Lung	lung
11	chr1:58088200-58090600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:58088200-58092200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr1:58088400-58089200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:58088400-58089200	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr1:58088400-58089800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr1:58088400-58089800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:58088400-58089800	Enhancers	Fetal Brain Female	brain
18	chr1:58088400-58089800	Enhancers	Fetal Stomach	stomach
19	chr1:58088400-58090000	Enhancers	Stomach Mucosa	stomach
20	chr1:58088400-58090200	Enhancers	H9 Cell Line	embryonic stem cell
21	chr1:58088400-58091000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:58088400-58092200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:58088400-58092200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:58088600-58089200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:58088800-58089600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:58088800-58089800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:58088800-58090000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:58088800-58090200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr1:58088800-58090200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:58088800-58091000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:58089000-58089200	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr1:58089000-58089600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:58089000-58089600	Enhancers	HepG2	liver
34	chr1:58089000-58090000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr1:58089000-58090200	Enhancers	HUES48 Cell Line	embryonic stem cell

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