Variant report

Variant	rs12425679
Chromosome Location	chr12:48549074-48549075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:48548411-48549200	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:48549006-48549115	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48496998..48499694-chr12:48547936..48550832,3	K562	blood:
2	chr12:48511519..48514886-chr12:48548320..48552889,5	K562	blood:
3	chr12:48548408..48551386-chr12:48576630..48579457,3	K562	blood:
4	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:
5	chr12:48545842..48549323-chr12:48549562..48552963,3	MCF-7	breast:

Variant related genes	Relation type
ASB8	TF binding region
ENSG00000177875	Chromatin interaction
ENSG00000079387	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000152556	Chromatin interaction

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

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

rs_ID	r²[population]
rs10492082	0.86[EUR][1000 genomes]
rs1049392	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747529	0.81[ASN][1000 genomes]
rs10875733	0.92[EUR][1000 genomes]
rs10875739	0.81[ASN][1000 genomes]
rs10875741	0.87[ASN][1000 genomes]
rs10875744	0.90[ASN][1000 genomes]
rs10875752	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875754	0.81[ASN][1000 genomes]
rs10875759	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10875761	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11168373	0.92[EUR][1000 genomes]
rs11168378	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11168404	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168412	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168417	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168419	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168424	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168434	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168435	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168438	0.84[ASN][1000 genomes]
rs11168439	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11168442	0.88[AMR][1000 genomes]
rs11168443	0.86[AMR][1000 genomes]
rs11168444	0.88[AMR][1000 genomes]
rs11168445	0.88[AMR][1000 genomes]
rs11168446	0.88[AMR][1000 genomes]
rs11168447	0.88[AMR][1000 genomes]
rs11168448	0.86[AMR][1000 genomes]
rs11168453	0.88[AMR][1000 genomes]
rs11168454	0.86[AMR][1000 genomes]
rs11834818	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12228924	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12422355	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12426981	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2107640	0.80[ASN][1000 genomes]
rs2158515	0.90[ASN][1000 genomes]
rs2240306	0.91[EUR][1000 genomes]
rs2286020	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742075	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56097189	0.82[ASN][1000 genomes]
rs56129148	0.82[ASN][1000 genomes]
rs57430775	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58540891	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58556309	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59537300	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59667534	0.87[EUR][1000 genomes]
rs6580658	0.86[AMR][1000 genomes]
rs66507954	0.88[AMR][1000 genomes]
rs7132898	0.86[ASN][1000 genomes]
rs7133274	0.83[AMR][1000 genomes]
rs7136243	0.88[AMR][1000 genomes]
rs7136782	0.86[AMR][1000 genomes]
rs7136788	0.88[AMR][1000 genomes]
rs7302354	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7303677	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7304428	0.87[ASN][1000 genomes]
rs73104071	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73304926	0.88[AMR][1000 genomes]
rs7484942	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7962390	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7962569	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8181670	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs886589	0.80[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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS 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	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48536800-48550800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:48537800-48550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:48538400-48550200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:48540400-48550000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:48540400-48550200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:48542200-48550400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:48543800-48550400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:48544000-48550000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:48544000-48550200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48544000-48550400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:48544000-48550400	Weak transcription	Esophagus	oesophagus
12	chr12:48544000-48550600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:48544200-48550400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:48544400-48550000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:48544400-48550400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:48544600-48550400	Weak transcription	Stomach Mucosa	stomach
17	chr12:48544800-48550200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:48545000-48550200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:48545200-48550000	Weak transcription	HUVEC	blood vessel
20	chr12:48545200-48550200	Weak transcription	Small Intestine	intestine
21	chr12:48545400-48550000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:48545400-48550200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:48545400-48550200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:48545400-48550200	Weak transcription	Fetal Heart	heart
25	chr12:48545600-48549600	Weak transcription	Pancreas	Pancrea
26	chr12:48545600-48550000	Weak transcription	Fetal Brain Male	brain
27	chr12:48545600-48550200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:48545600-48550200	Weak transcription	NHEK	skin
29	chr12:48545600-48550200	Weak transcription	NHLF	lung
30	chr12:48545600-48550400	Weak transcription	Aorta	Aorta
31	chr12:48545800-48550200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:48546200-48550000	Weak transcription	A549	lung
33	chr12:48546200-48550200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:48546200-48550200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:48546200-48550200	Weak transcription	Right Ventricle	heart
36	chr12:48546200-48550600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr12:48546400-48550000	Weak transcription	HepG2	liver
38	chr12:48546600-48549600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:48546800-48550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:48547000-48550200	Weak transcription	Fetal Kidney	kidney
41	chr12:48547200-48550000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:48547200-48550000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:48547200-48550000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:48547200-48550000	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:48547200-48550000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:48547200-48550000	Weak transcription	NH-A	brain
47	chr12:48547200-48550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:48547400-48549600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:48547400-48549600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:48547400-48549800	Weak transcription	Brain Germinal Matrix	brain

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