Variant report

Variant	rs9645814
Chromosome Location	chr12:39073964-39073965
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr12:39073812-39074012	MCF10A-Er-Src	breast:	n/a	chr12:39073954-39073977

Variant related genes	Relation type
CPNE8	TF binding region

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1021256	0.87[EUR][1000 genomes]
rs1021258	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1038540	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1038543	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10747574	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs10875959	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10875962	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875963	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095577	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11168552	0.87[ASN][1000 genomes]
rs11168979	0.97[ASN][1000 genomes]
rs11169037	0.81[YRI][hapmap]
rs11169095	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11169333	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169407	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12309958	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12318974	1.00[ASN][1000 genomes]
rs12322362	0.87[ASN][1000 genomes]
rs1472657	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1486349	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1486350	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1486351	0.93[EUR][1000 genomes]
rs1486352	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1486353	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1502631	0.87[ASN][1000 genomes]
rs1615569	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1619885	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1620594	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1620655	0.95[JPT][hapmap];1.00[EUR][1000 genomes]
rs1621467	1.00[EUR][1000 genomes]
rs1624751	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1684395	0.88[YRI][hapmap]
rs1684419	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1684420	0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs1684421	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1719846	0.95[JPT][hapmap];1.00[EUR][1000 genomes]
rs1719848	0.89[YRI][hapmap]
rs1827459	0.91[ASN][1000 genomes]
rs1843640	1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs1843641	1.00[EUR][1000 genomes]
rs1847181	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1906043	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2101370	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264357	0.98[ASN][1000 genomes]
rs2388058	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs2630778	0.81[YRI][hapmap]
rs2630779	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2653739	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2653757	0.97[ASN][1000 genomes]
rs2653762	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2653770	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2653777	0.87[ASN][1000 genomes]
rs2730891	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2730911	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2730923	0.87[ASN][1000 genomes]
rs2730931	1.00[CEU][hapmap];0.86[ASN][1000 genomes]
rs2730938	0.88[ASN][1000 genomes]
rs4238079	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4293160	1.00[JPT][hapmap]
rs4494336	0.96[EUR][1000 genomes]
rs4767968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5005131	1.00[JPT][hapmap]
rs7957523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976054	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs7980889	1.00[ASN][1000 genomes]
rs826864	0.87[EUR][1000 genomes]
rs826878	0.90[JPT][hapmap]
rs826881	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs826893	0.91[JPT][hapmap]
rs864324	0.91[JPT][hapmap]
rs923200	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9805091	0.87[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	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers 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	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1045040	chr12:39038114-39084094	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39046000-39085400	Weak transcription	Aorta	Aorta
2	chr12:39046800-39080400	Weak transcription	Spleen	Spleen
3	chr12:39051600-39080400	Weak transcription	Lung	lung
4	chr12:39051600-39080800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:39055800-39100800	Weak transcription	NHEK	skin
6	chr12:39056000-39080200	Weak transcription	Ovary	ovary
7	chr12:39056000-39092200	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
10	chr12:39056200-39078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:39056200-39078400	Weak transcription	Adipose Nuclei	Adipose
12	chr12:39056200-39079000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:39056200-39080200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:39056800-39083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:39057400-39083000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:39058000-39077600	Weak transcription	HMEC	breast
17	chr12:39058200-39079000	Weak transcription	GM12878-XiMat	blood
18	chr12:39061200-39080400	Weak transcription	A549	lung
19	chr12:39061600-39080200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:39063800-39080400	Weak transcription	Fetal Intestine Large	intestine
21	chr12:39063800-39082600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
23	chr12:39066600-39083400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:39067000-39076600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:39068600-39076400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:39069000-39079000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:39069000-39080400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:39069800-39076400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:39069800-39078600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:39069800-39083000	Weak transcription	Left Ventricle	heart
32	chr12:39071400-39077800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr12:39071600-39079200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:39071800-39075400	Weak transcription	Liver	Liver
35	chr12:39071800-39078000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:39071800-39078400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:39072200-39075800	Weak transcription	Monocytes-CD14+_RO01746	blood

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