Variant report

Variant	rs12925656
Chromosome Location	chr16:65107920-65107921
allele	C/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	POLR2A	chr16:65107148-65108037	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
CDH11	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10852420	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12708870	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs12708871	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1402017	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1879261	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1915116	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs257338	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[AMR][1000 genomes]
rs257488	1.00[CEU][hapmap]
rs257491	0.92[CEU][hapmap]
rs35147	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs35194	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs35196	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs40114	1.00[CEU][hapmap]
rs6416687	0.87[CEU][hapmap];0.89[AMR][1000 genomes]
rs6416688	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6416689	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs6498969	0.85[AMR][1000 genomes]
rs6498970	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs6498971	0.83[AMR][1000 genomes]
rs6498972	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6498975	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6498977	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7191190	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7206144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7404112	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7404568	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7498207	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs7498373	0.93[CEU][hapmap]
rs7499071	0.87[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs7499444	0.83[AMR][1000 genomes]
rs7500159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7500476	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes]
rs7500503	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs8051995	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs8054252	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9746754	0.83[AMR][1000 genomes]
rs9921084	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948640	chr16:64859061-65112790	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv833260	chr16:65050647-65218759	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:65095000-65113400	Weak transcription	Lung	lung
2	chr16:65095800-65152000	Weak transcription	Fetal Intestine Large	intestine
3	chr16:65103800-65108200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr16:65104600-65116200	Weak transcription	Fetal Intestine Small	intestine
5	chr16:65105200-65113400	Weak transcription	Fetal Kidney	kidney
6	chr16:65105400-65109600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr16:65105400-65117200	Weak transcription	HMEC	breast
8	chr16:65105600-65108200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr16:65106200-65108800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:65106200-65108800	Weak transcription	Fetal Brain Female	brain
11	chr16:65106200-65114200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr16:65106200-65115800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr16:65106200-65147400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr16:65106400-65108800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr16:65106400-65108800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr16:65106400-65108800	Weak transcription	Fetal Brain Male	brain
17	chr16:65106400-65108800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr16:65106400-65108800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr16:65106400-65109000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr16:65106400-65109800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr16:65106400-65115800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr16:65106400-65116800	Weak transcription	Brain Hippocampus Middle	brain
23	chr16:65106400-65120000	Weak transcription	Brain Germinal Matrix	brain
24	chr16:65106400-65120400	Weak transcription	Aorta	Aorta
25	chr16:65106400-65128400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr16:65106400-65147600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr16:65106600-65109800	Enhancers	Brain Anterior Caudate	brain
28	chr16:65106800-65108000	Strong transcription	Fetal Stomach	stomach
29	chr16:65106800-65108800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr16:65106800-65108800	Weak transcription	Brain Substantia Nigra	brain
31	chr16:65106800-65109000	Weak transcription	Fetal Muscle Leg	muscle
32	chr16:65106800-65112200	Strong transcription	Osteobl	bone
33	chr16:65106800-65115800	Weak transcription	HSMM	muscle
34	chr16:65106800-65132400	Weak transcription	HSMMtube	muscle
35	chr16:65106800-65151800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr16:65107000-65109600	Weak transcription	NH-A	brain
37	chr16:65107000-65110800	Strong transcription	Fetal Lung	lung
38	chr16:65107000-65115800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr16:65107000-65117000	Weak transcription	NHDF-Ad	bronchial
40	chr16:65107000-65124000	Weak transcription	NHLF	lung
41	chr16:65107000-65132400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr16:65107400-65108800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr16:65107400-65110000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr16:65107400-65132600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr16:65107600-65108000	Enhancers	Ovary	ovary
46	chr16:65107600-65108000	Enhancers	Spleen	Spleen
47	chr16:65107600-65108200	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr16:65107600-65109800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr16:65107800-65108000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr16:65107800-65108800	Weak transcription	Brain Angular Gyrus	brain

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