Variant report

Variant	rs28448423
Chromosome Location	chr12:12382236-12382237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12381851..12384074-chr12:12419779..12421401,2	K562	blood:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10082834	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083170	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10466847	1.00[ASN][1000 genomes]
rs10466848	1.00[ASN][1000 genomes]
rs10845497	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845499	0.92[EUR][1000 genomes]
rs10845500	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054695	1.00[ASN][1000 genomes]
rs11054696	1.00[ASN][1000 genomes]
rs11054702	1.00[ASN][1000 genomes]
rs11054705	1.00[ASN][1000 genomes]
rs11054706	1.00[ASN][1000 genomes]
rs11054707	1.00[ASN][1000 genomes]
rs11054709	1.00[ASN][1000 genomes]
rs11054710	1.00[ASN][1000 genomes]
rs11054713	1.00[ASN][1000 genomes]
rs11054720	0.87[EUR][1000 genomes]
rs11054729	0.96[EUR][1000 genomes]
rs11054732	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11054746	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054767	1.00[ASN][1000 genomes]
rs1123213	1.00[ASN][1000 genomes]
rs11829211	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831610	1.00[ASN][1000 genomes]
rs12296239	1.00[ASN][1000 genomes]
rs12297598	0.92[EUR][1000 genomes]
rs12304957	0.85[EUR][1000 genomes]
rs12305378	1.00[ASN][1000 genomes]
rs12306293	1.00[ASN][1000 genomes]
rs12306537	1.00[ASN][1000 genomes]
rs12307111	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309246	1.00[ASN][1000 genomes]
rs12309338	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12310020	1.00[ASN][1000 genomes]
rs12311202	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12311922	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316043	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12319942	0.96[EUR][1000 genomes]
rs12422890	1.00[ASN][1000 genomes]
rs12424332	1.00[ASN][1000 genomes]
rs12424361	1.00[ASN][1000 genomes]
rs12425185	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425699	1.00[ASN][1000 genomes]
rs12427198	0.89[EUR][1000 genomes]
rs13377971	1.00[ASN][1000 genomes]
rs16907789	1.00[ASN][1000 genomes]
rs56259928	1.00[ASN][1000 genomes]
rs56998126	0.96[EUR][1000 genomes]
rs57055264	0.87[EUR][1000 genomes]
rs58682800	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59386755	1.00[ASN][1000 genomes]
rs7308022	0.91[EUR][1000 genomes]
rs7311064	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061123	0.87[EUR][1000 genomes]
rs74061145	0.92[EUR][1000 genomes]
rs7957531	0.87[EUR][1000 genomes]
rs7960716	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7973583	0.91[EUR][1000 genomes]
rs7973718	0.90[EUR][1000 genomes]
rs7978064	0.85[EUR][1000 genomes]
rs7979919	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630249	1.00[ASN][1000 genomes]
rs9630250	1.00[ASN][1000 genomes]
rs9630266	1.00[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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12368200-12384200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:12370800-12392200	Weak transcription	Brain Substantia Nigra	brain
4	chr12:12374800-12383200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:12377400-12382400	Weak transcription	HSMM	muscle
6	chr12:12377800-12384200	Weak transcription	K562	blood
7	chr12:12377800-12407200	Weak transcription	NH-A	brain
8	chr12:12379200-12396800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:12379400-12382600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:12379400-12393600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:12379600-12384200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:12379600-12393600	Weak transcription	NHLF	lung
13	chr12:12379800-12382800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:12380000-12382400	Weak transcription	Fetal Kidney	kidney
15	chr12:12380000-12384200	Weak transcription	HepG2	liver
16	chr12:12380200-12384800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:12380200-12388800	Weak transcription	Fetal Intestine Small	intestine
18	chr12:12380400-12382600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:12380800-12382600	Weak transcription	Brain Angular Gyrus	brain
20	chr12:12380800-12388400	Weak transcription	Fetal Stomach	stomach
21	chr12:12381000-12383000	Enhancers	Brain Hippocampus Middle	brain
22	chr12:12381200-12383000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr12:12381200-12387400	Enhancers	Liver	Liver
24	chr12:12381400-12383400	Enhancers	Fetal Brain Female	brain
25	chr12:12381400-12393600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:12381600-12382600	Weak transcription	A549	lung
27	chr12:12381600-12383800	Weak transcription	Lung	lung
28	chr12:12381600-12384200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:12381600-12384600	Weak transcription	Left Ventricle	heart
30	chr12:12381600-12390000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:12381800-12383000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:12381800-12383000	Enhancers	Fetal Lung	lung
33	chr12:12381800-12383000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr12:12381800-12384200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:12381800-12384200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:12381800-12384600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr12:12381800-12391800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:12381800-12393000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:12382000-12382400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:12382000-12384200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:12382000-12384200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:12382000-12384200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:12382000-12384200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:12382000-12384600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:12382000-12384600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:12382000-12384600	Weak transcription	Ovary	ovary
47	chr12:12382000-12384600	Weak transcription	Right Atrium	heart
48	chr12:12382000-12389400	Weak transcription	Psoas Muscle	Psoas
49	chr12:12382000-12392000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:12382000-12393800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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