Variant report

Variant	rs12906612
Chromosome Location	chr15:72472278-72472279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72466458..72468561-chr15:72471988..72474307,2	MCF-7	breast:
2	chr15:72469515..72473441-chr15:72475665..72477509,3	K562	blood:
3	chr15:72471247..72473901-chr15:72474760..72477219,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175318	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10220850	1.00[CEU][hapmap]
rs10518987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10732234	1.00[AMR][1000 genomes]
rs11632505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12324744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12899442	0.84[ASN][1000 genomes]
rs12902160	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12904378	1.00[CEU][hapmap]
rs12904667	0.84[ASN][1000 genomes]
rs12905794	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12905947	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12906356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907087	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12907377	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12907707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12908241	0.94[ASN][1000 genomes]
rs12908863	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12908883	1.00[CEU][hapmap]
rs12909590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12910475	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12910620	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12911278	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12911285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12914208	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12914269	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12914312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12915008	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12916039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12916226	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12916298	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12916789	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12917402	0.84[ASN][1000 genomes]
rs12917442	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1426169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2277543	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2288257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2912203	0.94[ASN][1000 genomes]
rs2912204	0.94[ASN][1000 genomes]
rs2912215	0.94[ASN][1000 genomes]
rs2912221	1.00[CEU][hapmap]
rs2912222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2912223	1.00[CEU][hapmap]
rs2912224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2912225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2957751	0.88[ASN][1000 genomes]
rs2957752	0.94[ASN][1000 genomes]
rs2959916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2959917	0.94[ASN][1000 genomes]
rs2959918	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2959919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs2959923	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2959924	0.94[ASN][1000 genomes]
rs2959925	1.00[CEU][hapmap]
rs2959926	1.00[CEU][hapmap]
rs2959927	0.94[ASN][1000 genomes]
rs2959929	0.94[ASN][1000 genomes]
rs2959931	0.94[ASN][1000 genomes]
rs2959933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2959935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2959940	0.84[ASN][1000 genomes]
rs34023258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34115124	0.94[ASN][1000 genomes]
rs34211376	0.94[ASN][1000 genomes]
rs34294127	0.94[ASN][1000 genomes]
rs34346715	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34362323	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34382909	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34481625	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34505994	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34511502	0.94[ASN][1000 genomes]
rs34538801	0.94[ASN][1000 genomes]
rs34638996	1.00[AMR][1000 genomes]
rs34658339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34677662	0.94[ASN][1000 genomes]
rs34694253	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34705283	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34789424	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34815962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35061524	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35071085	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35104697	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35136885	1.00[AMR][1000 genomes]
rs35144689	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35202897	0.94[ASN][1000 genomes]
rs35259670	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35285520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35288005	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35362359	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35378070	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35408293	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35457238	0.94[ASN][1000 genomes]
rs35491098	0.81[ASN][1000 genomes]
rs35554838	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35694406	1.00[ASN][1000 genomes]
rs35836103	1.00[AMR][1000 genomes]
rs36110969	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3743227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3743228	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3743229	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3759817	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3759819	0.81[ASN][1000 genomes]
rs3759821	0.81[ASN][1000 genomes]
rs3759901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3825949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4776592	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4776593	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4777501	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs55935015	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs57420281	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57692836	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58352854	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66608810	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67195650	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71395049	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs71395050	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs71395056	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71395057	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71395058	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71395061	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71395066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71395068	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71395070	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71395074	0.94[ASN][1000 genomes]
rs71397231	0.94[ASN][1000 genomes]
rs71397232	0.94[ASN][1000 genomes]
rs71397233	0.94[ASN][1000 genomes]
rs71411063	0.94[ASN][1000 genomes]
rs7169150	1.00[ASN][1000 genomes]
rs7174264	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73438446	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8192359	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8192387	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8192397	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs890312	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9672916	1.00[CEU][hapmap]
rs9806184	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9806204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];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	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
6	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 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	chr15:72465000-72476200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr15:72466600-72472400	Enhancers	HMEC	breast
3	chr15:72466800-72476200	Weak transcription	Esophagus	oesophagus
4	chr15:72468000-72476000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:72468400-72473200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:72468400-72476000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:72469000-72475000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:72470200-72473600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:72471200-72473400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr15:72471200-72473800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:72471200-72474200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr15:72471200-72474400	Enhancers	Brain Anterior Caudate	brain
13	chr15:72471400-72473000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:72471400-72473200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr15:72471400-72473200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr15:72471400-72473400	Enhancers	Brain Angular Gyrus	brain
17	chr15:72471400-72473600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:72471400-72473800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:72471600-72472400	Enhancers	Lung	lung
20	chr15:72471600-72473000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:72471600-72473200	Enhancers	Fetal Muscle Leg	muscle
22	chr15:72471600-72473400	Enhancers	Brain Cingulate Gyrus	brain
23	chr15:72471600-72473600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:72471800-72473200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:72471800-72473400	Flanking Active TSS	HepG2	liver
26	chr15:72471800-72476200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:72472000-72472400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr15:72472000-72472400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:72472000-72472400	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr15:72472000-72472400	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr15:72472000-72472400	Enhancers	Gastric	stomach
32	chr15:72472000-72472400	Enhancers	Left Ventricle	heart
33	chr15:72472000-72472400	Enhancers	Pancreas	Pancrea
34	chr15:72472000-72472800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:72472000-72473000	Enhancers	Adipose Nuclei	Adipose
36	chr15:72472000-72473000	Enhancers	Right Atrium	heart
37	chr15:72472000-72474200	Weak transcription	A549	lung
38	chr15:72472000-72476200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:72472200-72472400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:72472200-72472400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr15:72472200-72472400	Enhancers	Fetal Heart	heart
42	chr15:72472200-72472400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
43	chr15:72472200-72472600	Enhancers	Brain Germinal Matrix	brain
44	chr15:72472200-72472600	Enhancers	Right Ventricle	heart
45	chr15:72472200-72472600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr15:72472200-72472600	Enhancers	Spleen	Spleen
47	chr15:72472200-72472800	Enhancers	Fetal Intestine Large	intestine
48	chr15:72472200-72472800	Enhancers	Fetal Intestine Small	intestine
49	chr15:72472200-72472800	Enhancers	Placenta Amnion	Placenta Amnion
50	chr15:72472200-72473000	Enhancers	Fetal Brain Female	brain

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