Variant report

Variant	rs1040270
Chromosome Location	chr16:65106437-65106438
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	JUND	chr16:65106376-65106576	HepG2	liver:	n/a	chr16:65106459-65106468 chr16:65106465-65106474
2	POLR2A	chr16:65105778-65106449	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
CDH11	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1025311	0.87[JPT][hapmap]
rs1040271	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10500508	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1079008	0.86[JPT][hapmap]
rs12935138	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1356823	0.82[ASN][1000 genomes]
rs1520229	0.93[JPT][hapmap]
rs1520230	0.93[JPT][hapmap]
rs1520231	0.86[JPT][hapmap]
rs1520232	0.89[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1520234	0.80[JPT][hapmap]
rs1520236	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1520243	0.93[JPT][hapmap]
rs1532418	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16968461	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs16968480	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1850966	0.85[EUR][1000 genomes]
rs1874457	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1915117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2088285	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2132543	0.92[ASN][1000 genomes]
rs2280396	0.88[CEU][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs257335	0.93[JPT][hapmap]
rs257336	0.93[JPT][hapmap]
rs257337	0.93[JPT][hapmap]
rs257341	0.86[JPT][hapmap]
rs257490	0.93[JPT][hapmap]
rs257497	0.87[JPT][hapmap]
rs257498	0.87[JPT][hapmap]
rs28216	0.92[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs34553411	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35054335	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35140	0.86[JPT][hapmap]
rs35144	0.87[JPT][hapmap]
rs35146	0.86[JPT][hapmap]
rs35148	0.86[JPT][hapmap]
rs35149	0.87[JPT][hapmap]
rs35150	0.87[JPT][hapmap]
rs35152	0.86[JPT][hapmap]
rs35154	0.87[JPT][hapmap]
rs35176	0.88[CEU][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs35188	0.87[JPT][hapmap]
rs35189	0.84[EUR][1000 genomes]
rs35191	0.86[JPT][hapmap]
rs35195	0.86[JPT][hapmap]
rs35198	0.86[JPT][hapmap]
rs35199	0.86[JPT][hapmap]
rs35200	0.86[JPT][hapmap]
rs35203	0.93[JPT][hapmap]
rs35204	0.87[JPT][hapmap]
rs35208	0.87[JPT][hapmap]
rs35209	0.82[JPT][hapmap]
rs35210	0.87[JPT][hapmap]
rs35214	0.86[JPT][hapmap]
rs35216	0.87[JPT][hapmap]
rs35219	0.87[JPT][hapmap]
rs35226	0.86[JPT][hapmap]
rs35709707	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40115	0.86[JPT][hapmap]
rs40116	0.86[JPT][hapmap]
rs42863	0.87[JPT][hapmap]
rs4393595	1.00[ASN][1000 genomes]
rs4967866	0.86[JPT][hapmap]
rs4967868	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4967882	0.93[JPT][hapmap]
rs4967884	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4967885	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4967886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59954387	0.81[EUR][1000 genomes]
rs7204729	0.87[CHB][hapmap];0.90[ASN][1000 genomes]
rs7498801	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8048351	0.96[ASN][1000 genomes]
rs878359	0.93[JPT][hapmap]
rs909003	0.86[JPT][hapmap]
rs973200	0.87[JPT][hapmap]
rs974782	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9935608	0.93[JPT][hapmap]

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:51 , 50 per page) page: 1 2

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	chr16:65104200-65107000	Genic enhancers	Fetal Lung	lung
5	chr16:65104600-65106800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr16:65104600-65116200	Weak transcription	Fetal Intestine Small	intestine
7	chr16:65104800-65106800	Genic enhancers	Fetal Stomach	stomach
8	chr16:65105200-65113400	Weak transcription	Fetal Kidney	kidney
9	chr16:65105400-65107000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr16:65105400-65109600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr16:65105400-65117200	Weak transcription	HMEC	breast
12	chr16:65105600-65107600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr16:65105600-65108200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr16:65105800-65106600	Flanking Active TSS	Brain Angular Gyrus	brain
15	chr16:65106000-65106600	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr16:65106000-65107000	Enhancers	NH-A	brain
17	chr16:65106200-65106800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr16:65106200-65106800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr16:65106200-65106800	Enhancers	Fetal Muscle Leg	muscle
20	chr16:65106200-65106800	Genic enhancers	Osteobl	bone
21	chr16:65106200-65107000	Enhancers	NHDF-Ad	bronchial
22	chr16:65106200-65107400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr16:65106200-65107400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr16:65106200-65108800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:65106200-65108800	Weak transcription	Fetal Brain Female	brain
26	chr16:65106200-65114200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr16:65106200-65115800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr16:65106200-65147400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr16:65106400-65106600	Enhancers	Brain Substantia Nigra	brain
30	chr16:65106400-65106800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr16:65106400-65106800	Enhancers	HSMM	muscle
32	chr16:65106400-65106800	Enhancers	HSMMtube	muscle
33	chr16:65106400-65107000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr16:65106400-65107000	Enhancers	NHLF	lung
35	chr16:65106400-65107400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr16:65106400-65107600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr16:65106400-65107600	Weak transcription	Ovary	ovary
38	chr16:65106400-65107600	Weak transcription	Spleen	Spleen
39	chr16:65106400-65108800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr16:65106400-65108800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr16:65106400-65108800	Weak transcription	Fetal Brain Male	brain
42	chr16:65106400-65108800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr16:65106400-65108800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr16:65106400-65109000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr16:65106400-65109800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr16:65106400-65115800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr16:65106400-65116800	Weak transcription	Brain Hippocampus Middle	brain
48	chr16:65106400-65120000	Weak transcription	Brain Germinal Matrix	brain
49	chr16:65106400-65120400	Weak transcription	Aorta	Aorta
50	chr16:65106400-65128400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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