Variant report

Variant	rs12080949
Chromosome Location	chr1:214847349-214847350
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11120374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120375	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088866	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168041	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290199	1.00[CEU][hapmap];0.95[ASN][1000 genomes]
rs335526	0.83[ASN][1000 genomes]
rs60411163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6687966	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083621	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73083625	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73083633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73083635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73083645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73083650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73083653	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542458	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921366	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004475	chr1:214763778-215013375	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1005669	chr1:214774522-214994142	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv997864	chr1:214778658-214994142	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1002937	chr1:214793813-214994142	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1013284	chr1:214799847-214951184	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv873165	chr1:214802299-214889859	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214804000-214858200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:214810400-214847400	Weak transcription	Brain Germinal Matrix	brain
3	chr1:214833400-214851600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:214835200-214847400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:214840400-214848600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:214840400-214850200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:214840400-214851600	Weak transcription	NH-A	brain
8	chr1:214840400-214851800	Weak transcription	NHDF-Ad	bronchial
9	chr1:214840600-214848000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:214840600-214851600	Weak transcription	HUVEC	blood vessel
11	chr1:214840600-214851800	Weak transcription	Osteobl	bone
12	chr1:214841000-214851200	Weak transcription	HSMM	muscle
13	chr1:214841400-214847400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:214841400-214850200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:214841400-214857000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:214842200-214856800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:214843000-214857000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:214843800-214847600	Weak transcription	Fetal Thymus	thymus
19	chr1:214844000-214847800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:214844000-214857000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:214844800-214847400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:214845000-214847400	Weak transcription	Fetal Heart	heart
23	chr1:214845400-214856800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:214845600-214857000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:214845800-214847400	Weak transcription	Dnd41	blood
26	chr1:214846000-214851400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:214846000-214856800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:214846000-214856800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:214846200-214848000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:214846200-214851800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:214846200-214857000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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