Variant report

Variant	rs12140023
Chromosome Location	chr1:103480387-103480388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1012283	0.81[AMR][1000 genomes]
rs11164661	0.84[EUR][1000 genomes]
rs12116763	0.84[EUR][1000 genomes]
rs12116792	0.84[EUR][1000 genomes]
rs12118796	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12119459	0.82[AMR][1000 genomes]
rs12119971	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12121661	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12121762	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12122632	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12123205	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12124555	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12124588	0.81[AMR][1000 genomes]
rs12127576	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12128196	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12129078	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12130683	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12131097	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12131383	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12131399	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12131769	0.84[EUR][1000 genomes]
rs12131957	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12132053	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12135531	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12136577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12136748	0.81[AMR][1000 genomes]
rs12136865	0.84[EUR][1000 genomes]
rs12138447	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12140064	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12140473	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12142411	0.84[EUR][1000 genomes]
rs12142524	0.82[AMR][1000 genomes]
rs12143676	0.81[AMR][1000 genomes]
rs12145647	0.82[EUR][1000 genomes]
rs12743365	0.81[AMR][1000 genomes]
rs1337181	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1337184	0.84[EUR][1000 genomes]
rs1337185	0.84[EUR][1000 genomes]
rs1337187	0.84[EUR][1000 genomes]
rs1337189	0.84[EUR][1000 genomes]
rs13375668	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1415349	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1415353	0.84[EUR][1000 genomes]
rs1415354	0.84[EUR][1000 genomes]
rs17447925	0.81[AMR][1000 genomes]
rs17507469	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1953672	0.84[EUR][1000 genomes]
rs1953673	0.84[EUR][1000 genomes]
rs1953674	0.84[EUR][1000 genomes]
rs2622857	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34277983	0.82[AMR][1000 genomes]
rs4353117	0.81[AMR][1000 genomes]
rs4489579	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4497231	0.83[EUR][1000 genomes]
rs4908285	0.88[EUR][1000 genomes]
rs58982976	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61816504	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61816509	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61816511	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61816512	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61816513	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61816515	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61816516	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61817081	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61817082	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61817084	0.84[EUR][1000 genomes]
rs61817085	0.84[EUR][1000 genomes]
rs61817086	0.82[EUR][1000 genomes]
rs6577346	0.84[EUR][1000 genomes]
rs6577347	0.84[EUR][1000 genomes]
rs6577348	0.84[EUR][1000 genomes]
rs6577349	0.84[EUR][1000 genomes]
rs6668897	0.84[EUR][1000 genomes]
rs9645399	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv870600	chr1:103336601-103548497	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871475	chr1:103339272-103548497	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv871741	chr1:103352451-103517428	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv871078	chr1:103352451-103548497	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv870607	chr1:103362909-103528128	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv870995	chr1:103384610-103548497	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv871372	chr1:103403752-103564540	Strong transcription Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv871067	chr1:103407999-103509323	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv871736	chr1:103409100-103548497	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv871567	chr1:103416690-103499049	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv871657	chr1:103427381-103528128	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv871198	chr1:103432687-103498029	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv546935	chr1:103438795-103498029	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv462772	chr1:103438795-103499896	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv546936	chr1:103438795-103499896	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv462783	chr1:103438795-103548497	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv546937	chr1:103438795-103548497	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv462794	chr1:103450196-103539007	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv546938	chr1:103450196-103539007	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv871286	chr1:103455217-103528128	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv830893	chr1:103458498-103635579	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv871733	chr1:103459537-103509323	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv871071	chr1:103471962-103509323	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv871365	chr1:103476179-103548497	Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv947194	chr1:103479322-103482565	Weak transcription Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103369600-103498600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:103386200-103482000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:103415800-103485200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:103446800-103497800	Weak transcription	HSMM	muscle
5	chr1:103449200-103545200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:103453400-103490000	Weak transcription	NH-A	brain
7	chr1:103460200-103516400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:103469800-103486600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:103471400-103486600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:103474800-103483600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:103475800-103516600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:103476200-103486800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:103477600-103484800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:103479400-103487000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:103479800-103480600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:103480200-103480400	Enhancers	Pancreatic Islets	Pancreatic Islet

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