Variant report

Variant	rs12422890
Chromosome Location	chr12:12304648-12304649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12287758..12289771-chr12:12301948..12304913,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10082834	1.00[ASN][1000 genomes]
rs10466847	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466848	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772531	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10845497	1.00[ASN][1000 genomes]
rs10845500	1.00[ASN][1000 genomes]
rs11054695	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054696	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054702	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054705	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054706	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054707	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054709	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054710	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054713	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	1.00[ASN][1000 genomes]
rs11054767	1.00[ASN][1000 genomes]
rs1123213	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829211	1.00[ASN][1000 genomes]
rs11831610	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12296239	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305378	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306293	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306537	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	1.00[ASN][1000 genomes]
rs12309246	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309338	1.00[ASN][1000 genomes]
rs12309495	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12310020	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311202	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311922	1.00[ASN][1000 genomes]
rs12316043	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424332	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424361	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425185	1.00[ASN][1000 genomes]
rs12425699	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377971	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907789	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448423	1.00[ASN][1000 genomes]
rs56259928	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	1.00[ASN][1000 genomes]
rs59386755	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	1.00[ASN][1000 genomes]
rs7979919	1.00[ASN][1000 genomes]
rs9630249	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630250	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630266	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
3	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:12271400-12306600	Weak transcription	Small Intestine	intestine
6	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
7	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:12272600-12305000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:12274600-12313600	Weak transcription	Colonic Mucosa	Colon
10	chr12:12277400-12306800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:12277600-12311600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:12278200-12310600	Weak transcription	Hela-S3	cervix
13	chr12:12279800-12311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:12279800-12311000	Weak transcription	HMEC	breast
15	chr12:12279800-12311600	Weak transcription	Dnd41	blood
16	chr12:12279800-12313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
19	chr12:12283400-12309200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:12285000-12309800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:12285000-12311400	Weak transcription	Pancreas	Pancrea
22	chr12:12285600-12315000	Weak transcription	Fetal Heart	heart
23	chr12:12287400-12318200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:12288200-12310600	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:12288200-12342800	Weak transcription	K562	blood
26	chr12:12288600-12311400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:12289400-12318200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:12297200-12318000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:12297600-12321400	Weak transcription	Gastric	stomach
30	chr12:12298000-12306000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:12298000-12308400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:12298800-12312200	Strong transcription	Fetal Intestine Large	intestine
33	chr12:12299000-12305800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:12299200-12310200	Strong transcription	Fetal Muscle Leg	muscle
35	chr12:12300000-12305200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr12:12300600-12315800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:12300800-12313200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:12301800-12308200	Weak transcription	Placenta	Placenta
39	chr12:12302000-12310200	Weak transcription	NHDF-Ad	bronchial
40	chr12:12302000-12311400	Weak transcription	Aorta	Aorta
41	chr12:12302000-12311800	Weak transcription	Lung	lung
42	chr12:12302000-12318000	Weak transcription	Stomach Mucosa	stomach
43	chr12:12302200-12325000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:12302200-12338400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr12:12302400-12313000	Weak transcription	NHLF	lung
46	chr12:12302600-12304800	Weak transcription	Fetal Stomach	stomach
47	chr12:12302600-12306800	Weak transcription	Fetal Intestine Small	intestine
48	chr12:12302600-12311400	Weak transcription	Brain Angular Gyrus	brain
49	chr12:12302800-12311400	Weak transcription	Fetal Brain Female	brain
50	chr12:12302800-12317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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