Variant report

Variant	rs28589663
Chromosome Location	chr12:57379616-57379617
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57374244..57376394-chr12:57378626..57381125,2	MCF-7	breast:
2	chr12:57347827..57349628-chr12:57379616..57381539,3	MCF-7	breast:
3	chr12:57350735..57353259-chr12:57379403..57381219,3	MCF-7	breast:
4	chr12:57156608..57159061-chr12:57379164..57381627,2	MCF-7	breast:
5	chr12:57378196..57379774-chr12:57392369..57394699,2	MCF-7	breast:
6	chr12:57144393..57147298-chr12:57377477..57379944,2	MCF-7	breast:
7	chr12:57232928..57235574-chr12:57379321..57382266,3	MCF-7	breast:
8	chr12:57023280..57025743-chr12:57378551..57381481,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000025423	Chromatin interaction
ENSG00000076108	Chromatin interaction
ENSG00000198056	Chromatin interaction
ENSG00000139547	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10400412	0.96[ASN][1000 genomes]
rs10400555	0.96[ASN][1000 genomes]
rs1044939	0.86[ASN][1000 genomes]
rs10506347	0.87[EUR][1000 genomes]
rs10506350	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10506351	0.86[ASN][1000 genomes]
rs1072670	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11832487	0.95[ASN][1000 genomes]
rs11834851	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11834856	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11836517	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12099695	0.97[ASN][1000 genomes]
rs12810024	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12810837	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12812499	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12815538	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12818342	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12824682	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12827039	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12827286	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1552245	0.91[ASN][1000 genomes]
rs17119301	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17119327	0.96[ASN][1000 genomes]
rs17119330	0.96[ASN][1000 genomes]
rs17119344	0.89[ASN][1000 genomes]
rs17119352	0.91[ASN][1000 genomes]
rs17119386	0.90[ASN][1000 genomes]
rs17119388	0.90[ASN][1000 genomes]
rs17119390	0.89[ASN][1000 genomes]
rs17119407	0.84[ASN][1000 genomes]
rs17119416	0.81[ASN][1000 genomes]
rs1843311	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1843312	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1843313	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2167306	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2270736	0.89[ASN][1000 genomes]
rs2270737	0.91[ASN][1000 genomes]
rs2270739	0.90[ASN][1000 genomes]
rs2279373	0.97[ASN][1000 genomes]
rs2279743	0.99[ASN][1000 genomes]
rs2291855	0.96[ASN][1000 genomes]
rs2371717	0.95[ASN][1000 genomes]
rs2888139	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34186462	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34253098	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34359134	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34762603	0.81[ASN][1000 genomes]
rs34969650	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35034299	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35243318	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35493121	0.97[ASN][1000 genomes]
rs3782329	0.90[ASN][1000 genomes]
rs3782330	0.90[ASN][1000 genomes]
rs3803018	0.92[ASN][1000 genomes]
rs3894415	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4016338	0.95[ASN][1000 genomes]
rs4039	0.86[ASN][1000 genomes]
rs4143085	0.90[ASN][1000 genomes]
rs56128678	0.89[ASN][1000 genomes]
rs56270558	0.89[ASN][1000 genomes]
rs56354404	0.89[ASN][1000 genomes]
rs57056392	0.90[ASN][1000 genomes]
rs57129030	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57351760	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57558853	0.96[ASN][1000 genomes]
rs58298943	0.99[ASN][1000 genomes]
rs58389529	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60258120	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60273384	0.97[ASN][1000 genomes]
rs60380217	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61504157	0.90[ASN][1000 genomes]
rs67476535	0.97[ASN][1000 genomes]
rs67771054	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67844278	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68126184	0.99[ASN][1000 genomes]
rs697222	0.80[ASN][1000 genomes]
rs7135297	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7136770	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71461303	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72482268	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298475	0.81[ASN][1000 genomes]
rs73114426	0.96[ASN][1000 genomes]
rs73114428	0.96[ASN][1000 genomes]
rs73114434	0.96[ASN][1000 genomes]
rs73114436	0.96[ASN][1000 genomes]
rs73114437	0.91[ASN][1000 genomes]
rs73114446	0.91[ASN][1000 genomes]
rs73114452	0.91[ASN][1000 genomes]
rs73114457	0.89[ASN][1000 genomes]
rs73114459	0.89[ASN][1000 genomes]
rs73114467	0.89[ASN][1000 genomes]
rs73114468	0.89[ASN][1000 genomes]
rs73114472	0.86[ASN][1000 genomes]
rs73116494	0.81[ASN][1000 genomes]
rs73116501	0.81[ASN][1000 genomes]
rs73131120	0.96[ASN][1000 genomes]
rs733629	0.96[ASN][1000 genomes]
rs746049	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7487948	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs754398	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs755221	0.89[ASN][1000 genomes]
rs7956166	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961920	0.90[ASN][1000 genomes]
rs7962771	0.81[ASN][1000 genomes]
rs7969312	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7972615	0.95[ASN][1000 genomes]
rs901068	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv1051116	chr12:57331370-57380365	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv899109	chr12:57331741-57381259	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv559021	chr12:57338716-57381259	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
6	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	esv15919	chr12:57374348-57379880	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv983334	chr12:57377803-57380748	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57361800-57389000	Weak transcription	Aorta	Aorta
2	chr12:57370800-57379800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:57370800-57381200	Weak transcription	Brain Anterior Caudate	brain
4	chr12:57371600-57381000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:57372000-57384800	Weak transcription	Gastric	stomach
6	chr12:57372200-57384800	Weak transcription	Primary T cells from cord blood	blood
7	chr12:57372600-57381000	Weak transcription	Spleen	Spleen
8	chr12:57372800-57381000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:57373200-57388600	Weak transcription	Fetal Brain Female	brain
10	chr12:57373200-57388800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:57374400-57379800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:57374600-57379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:57374600-57379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:57375200-57381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:57375600-57379800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:57377000-57381000	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:57377000-57395200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:57379200-57382400	Enhancers	NHEK	skin
19	chr12:57379600-57379800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:57379600-57379800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:57379600-57379800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:57379600-57379800	Enhancers	NH-A	brain
23	chr12:57379600-57380000	Enhancers	HSMMtube	muscle
24	chr12:57379600-57380200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:57379600-57380200	Enhancers	Placenta	Placenta
26	chr12:57379600-57380200	Enhancers	Thymus	Thymus
27	chr12:57379600-57380200	Enhancers	Hela-S3	cervix
28	chr12:57379600-57380200	Enhancers	HepG2	liver
29	chr12:57379600-57380400	Enhancers	A549	lung
30	chr12:57379600-57380600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr12:57379600-57381400	Enhancers	HMEC	breast
32	chr12:57379600-57381400	Enhancers	K562	blood
33	chr12:57379600-57382400	Enhancers	Fetal Thymus	thymus

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