Variant report

Variant	rs7960638
Chromosome Location	chr12:117482799-117482800
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	chr12:117397026..117399218-chr12:117481554..117483572,2	MCF-7	breast:
2	chr12:117478574..117480262-chr12:117481796..117483489,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10744887	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774899	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850745	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850746	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10850747	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10850751	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10850752	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068299	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068300	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068301	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068306	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611741	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11832441	0.82[EUR][1000 genomes]
rs11834817	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837022	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12368876	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472523	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2062528	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2173654	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291911	0.86[EUR][1000 genomes]
rs2393124	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782191	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782192	0.84[EUR][1000 genomes]
rs4766825	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55969361	0.82[EUR][1000 genomes]
rs58470318	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59756806	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6490104	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490105	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6490106	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6490107	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7294692	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297303	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7297917	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7953553	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956481	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960731	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964668	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7964686	0.81[EUR][1000 genomes]
rs7968761	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7968891	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971795	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972416	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978810	0.82[EUR][1000 genomes]
rs9634171	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1804583	chr12:117472107-117525169	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117467400-117486000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:117470800-117483400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:117471200-117482800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:117472600-117483000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:117476400-117484600	Weak transcription	Dnd41	blood
6	chr12:117477400-117482800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:117477400-117482800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:117477400-117483000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:117477400-117484800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr12:117477600-117482800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:117477800-117482800	Weak transcription	Fetal Brain Female	brain
12	chr12:117478000-117482800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:117478200-117482800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:117478200-117482800	Weak transcription	Brain Anterior Caudate	brain
15	chr12:117478200-117482800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:117478400-117482800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:117479600-117488000	Enhancers	Fetal Heart	heart
18	chr12:117480200-117482800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr12:117480400-117482800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:117480400-117483400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:117480400-117485800	Weak transcription	Right Atrium	heart
22	chr12:117480600-117483000	Weak transcription	Spleen	Spleen
23	chr12:117480600-117484000	Weak transcription	Pancreas	Pancrea
24	chr12:117480600-117485800	Weak transcription	Ovary	ovary
25	chr12:117480600-117486200	Weak transcription	Esophagus	oesophagus
26	chr12:117480800-117482800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:117480800-117483200	Weak transcription	HSMMtube	muscle
28	chr12:117480800-117484200	Weak transcription	Gastric	stomach
29	chr12:117481000-117483000	Weak transcription	Right Ventricle	heart
30	chr12:117481200-117482800	Weak transcription	Fetal Intestine Small	intestine
31	chr12:117481200-117482800	Enhancers	K562	blood
32	chr12:117481200-117485600	Weak transcription	A549	lung
33	chr12:117481200-117485600	Weak transcription	Hela-S3	cervix
34	chr12:117481400-117482800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:117481400-117486000	Weak transcription	Stomach Mucosa	stomach
36	chr12:117481600-117483400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:117481800-117482800	Weak transcription	Fetal Intestine Large	intestine
38	chr12:117482000-117483000	Bivalent Enhancer	Placenta	Placenta
39	chr12:117482000-117484600	Enhancers	Left Ventricle	heart
40	chr12:117482200-117483400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:117482200-117484400	Enhancers	Primary hematopoietic stem cells	blood
42	chr12:117482200-117485000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr12:117482400-117484000	Enhancers	Fetal Muscle Leg	muscle
44	chr12:117482400-117484400	Enhancers	Fetal Thymus	thymus
45	chr12:117482600-117482800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:117482600-117482800	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr12:117482600-117483400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr12:117482600-117483600	Enhancers	Primary B cells from peripheral blood	blood
49	chr12:117482600-117483600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
50	chr12:117482600-117484000	Enhancers	Cortex derived primary cultured neurospheres	brain

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