Variant report

Variant	rs12425787
Chromosome Location	chr12:1645204-1645205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1631412..1633755-chr12:1644616..1647066,2	K562	blood:
2	chr12:1643386..1645620-chr12:1647542..1650042,3	K562	blood:
3	chr12:1642084..1645971-chr12:1702065..1704505,3	K562	blood:

Variant related genes	Relation type
ENSG00000171823	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10848508	0.84[EUR][1000 genomes]
rs10848509	0.84[EUR][1000 genomes]
rs11061824	0.90[ASN][1000 genomes]
rs11061826	0.90[ASN][1000 genomes]
rs11061827	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11061828	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11061829	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11061831	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11061832	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11061838	0.87[ASN][1000 genomes]
rs12369458	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12369488	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12423119	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12424681	0.90[ASN][1000 genomes]
rs12424696	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12425641	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1046134	chr12:1153489-1675223	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS 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	16 gene(s)	inside rSNPs	diseases
4	nsv541344	chr12:1153489-1675223	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS 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
5	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised 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 miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1054178	chr12:1372157-1682699	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv541347	chr12:1372157-1682699	Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	esv3397478	chr12:1535455-1730159	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS 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
10	nsv1049247	chr12:1566534-1671806	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv1039629	chr12:1608565-1681391	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv541349	chr12:1608565-1681391	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv898585	chr12:1611846-1674239	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv826180	chr12:1614395-1759431	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
16	esv1808027	chr12:1618365-1645257	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv1824458	chr12:1618365-1645257	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	esv1826568	chr12:1618365-1645257	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	esv1836167	chr12:1618365-1645257	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv826181	chr12:1619798-1754941	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	nsv1052624	chr12:1637913-1667581	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	esv2762959	chr12:1637913-1680951	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1641400-1646000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:1641400-1649200	Weak transcription	HMEC	breast
3	chr12:1643200-1649400	Weak transcription	NHEK	skin
4	chr12:1643200-1650800	Weak transcription	Esophagus	oesophagus
5	chr12:1643400-1647000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:1643400-1647200	Weak transcription	Ovary	ovary
7	chr12:1643400-1657400	Weak transcription	K562	blood
8	chr12:1643400-1662400	Weak transcription	Fetal Brain Female	brain
9	chr12:1643400-1668400	Weak transcription	Fetal Brain Male	brain
10	chr12:1644200-1649200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:1644400-1645600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:1644400-1646600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:1644400-1649200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:1644600-1645400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:1644600-1649800	Weak transcription	HSMM	muscle
16	chr12:1644800-1645800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:1644800-1645800	Weak transcription	GM12878-XiMat	blood
18	chr12:1644800-1646000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:1644800-1649800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:1644800-1649800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:1644800-1659200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:1645000-1648800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:1645000-1649600	Weak transcription	Osteobl	bone
24	chr12:1645200-1645400	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr12:1645200-1646400	Strong transcription	NHDF-Ad	bronchial
26	chr12:1645200-1646400	Weak transcription	NHLF	lung

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