Variant report

Variant	rs12426981
Chromosome Location	chr12:48471268-48471269
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48471151..48472843-chr12:48551945..48554852,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258051	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10492082	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1049392	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10747529	0.85[ASN][1000 genomes]
rs10875726	0.81[ASN][1000 genomes]
rs10875727	0.81[ASN][1000 genomes]
rs10875733	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875739	0.85[ASN][1000 genomes]
rs10875752	0.85[EUR][1000 genomes]
rs11168361	0.83[ASN][1000 genomes]
rs11168363	0.84[ASN][1000 genomes]
rs11168364	0.84[ASN][1000 genomes]
rs11168373	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168378	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168404	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168412	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168417	0.91[EUR][1000 genomes]
rs11168419	0.91[EUR][1000 genomes]
rs11168424	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11168434	0.86[EUR][1000 genomes]
rs11168435	0.86[EUR][1000 genomes]
rs11834818	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228924	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12422355	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425679	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1859440	0.80[ASN][1000 genomes]
rs1978161	0.92[ASN][1000 genomes]
rs2056448	0.81[ASN][1000 genomes]
rs2107640	0.84[ASN][1000 genomes]
rs2240306	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286020	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2408954	0.82[ASN][1000 genomes]
rs3742075	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825403	0.93[ASN][1000 genomes]
rs4258439	0.93[ASN][1000 genomes]
rs4760678	0.86[ASN][1000 genomes]
rs56129148	0.81[ASN][1000 genomes]
rs57430775	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs58540891	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58556309	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs59667534	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7138917	0.93[ASN][1000 genomes]
rs7299704	0.85[ASN][1000 genomes]
rs7302354	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7303677	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73104071	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs733592	0.80[ASN][1000 genomes]
rs765260	0.81[ASN][1000 genomes]
rs886589	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	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
3	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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
3	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
5	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:48444200-48474600	Weak transcription	Gastric	stomach
7	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:48453800-48474800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:48454600-48478800	Weak transcription	Pancreas	Pancrea
11	chr12:48454800-48472000	Strong transcription	Dnd41	blood
12	chr12:48457400-48482000	Weak transcription	Right Ventricle	heart
13	chr12:48457600-48478600	Weak transcription	HSMMtube	muscle
14	chr12:48459200-48479000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:48463600-48476200	Weak transcription	HUVEC	blood vessel
16	chr12:48464400-48476200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:48464600-48472600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:48464600-48489400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:48464800-48476000	Weak transcription	Fetal Brain Male	brain
20	chr12:48464800-48482400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:48465000-48474000	Weak transcription	Lung	lung
22	chr12:48465000-48474600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:48465000-48477000	Weak transcription	Brain Angular Gyrus	brain
24	chr12:48465000-48478800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:48465000-48478800	Weak transcription	Aorta	Aorta
26	chr12:48465000-48487400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:48465800-48476800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:48466200-48481400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:48466400-48472600	Weak transcription	Ovary	ovary
30	chr12:48466800-48472600	Weak transcription	Fetal Intestine Small	intestine
31	chr12:48466800-48472600	Weak transcription	Fetal Stomach	stomach
32	chr12:48466800-48478800	Weak transcription	Esophagus	oesophagus
33	chr12:48468200-48472400	Weak transcription	NHLF	lung
34	chr12:48468200-48472600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:48468200-48472600	Weak transcription	Hela-S3	cervix
36	chr12:48468200-48476000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:48468200-48476000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:48468200-48476000	Weak transcription	HSMM	muscle
39	chr12:48468200-48478800	Weak transcription	HepG2	liver
40	chr12:48468400-48471400	Weak transcription	Fetal Brain Female	brain
41	chr12:48468400-48472600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:48468400-48472600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:48468400-48474000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:48468400-48474000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:48468400-48474200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:48468400-48474200	Weak transcription	Spleen	Spleen
47	chr12:48468400-48474600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:48468400-48474600	Weak transcription	GM12878-XiMat	blood
49	chr12:48468400-48476000	Weak transcription	Fetal Lung	lung
50	chr12:48468400-48476200	Weak transcription	Brain Hippocampus Middle	brain

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