Variant report

Variant	rs2029169
Chromosome Location	chr12:24912517-24912518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10743516	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771118	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047587	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1154753	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1155525	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1386644	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466585	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466586	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466587	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466589	0.87[EUR][1000 genomes]
rs1487665	0.87[EUR][1000 genomes]
rs1487666	0.87[EUR][1000 genomes]
rs1565121	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1601765	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872648	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994434	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2101371	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2200510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963588	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963786	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306537	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965973	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974523	1.00[ASN][1000 genomes]
rs7979271	1.00[ASN][1000 genomes]
rs7980180	1.00[ASN][1000 genomes]
rs901710	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1046463	chr12:24538432-24916851	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv898920	chr12:24648863-25147192	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv915555	chr12:24666481-24952013	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv1053309	chr12:24770995-25078227	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS 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	11 gene(s)	inside rSNPs	diseases
9	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv470278	chr12:24878591-24925239	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1041221	chr12:24880443-25213168	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
13	nsv541425	chr12:24880443-25213168	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv469170	chr12:24891175-25204353	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv557776	chr12:24891175-25204353	Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv557777	chr12:24891175-25205241	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	nsv469173	chr12:24891175-25207653	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv557778	chr12:24891175-25207653	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	nsv826283	chr12:24902154-24965379	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:24901600-24912800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr12:24903800-24912600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:24907800-24914600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:24908200-24913000	Enhancers	HepG2	liver
5	chr12:24908200-24913200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr12:24908400-24912800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:24908400-24912800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:24908400-24913600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:24908600-24912800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:24908600-24913600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:24908800-24912600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:24909400-24912800	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:24910200-24912800	Weak transcription	Brain Substantia Nigra	brain
14	chr12:24910200-24913000	Weak transcription	Fetal Lung	lung
15	chr12:24910200-24914200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:24910600-24912600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:24910800-24912800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:24911200-24914400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr12:24911400-24912800	Enhancers	K562	blood
20	chr12:24911800-24913000	Weak transcription	Brain Angular Gyrus	brain
21	chr12:24912000-24912800	Enhancers	HSMM	muscle
22	chr12:24912000-24913000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:24912000-24914000	Enhancers	HMEC	breast
24	chr12:24912000-24914400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:24912200-24912600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:24912200-24913000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:24912200-24914400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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