Variant report

Variant	rs11196959
Chromosome Location	chr10:116640176-116640177
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	chr10:116639834..116644233-chr10:116697414..116700996,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165832	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10490909	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10885613	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10885614	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10885615	0.81[ASN][1000 genomes]
rs10885616	0.81[ASN][1000 genomes]
rs10885620	0.88[ASN][1000 genomes]
rs10885622	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196924	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11196929	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196930	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196932	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196935	0.86[ASN][1000 genomes]
rs11196936	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196937	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196939	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196940	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196941	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196942	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11196943	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196944	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196945	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11196947	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196948	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196950	0.94[ASN][1000 genomes]
rs11196951	0.96[ASN][1000 genomes]
rs11196952	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196953	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196954	0.81[ASN][1000 genomes]
rs11196955	0.81[ASN][1000 genomes]
rs11196956	0.81[ASN][1000 genomes]
rs11196957	0.81[ASN][1000 genomes]
rs11196962	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11819372	0.88[ASN][1000 genomes]
rs12218498	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12411629	0.81[ASN][1000 genomes]
rs12414613	0.81[ASN][1000 genomes]
rs12415173	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1359079	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1359080	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17095662	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17586888	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17663387	0.88[ASN][1000 genomes]
rs17663670	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1924034	0.88[ASN][1000 genomes]
rs2016966	0.81[ASN][1000 genomes]
rs2146805	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2181563	0.86[ASN][1000 genomes]
rs2286632	0.81[ASN][1000 genomes]
rs2420065	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2420066	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2420067	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2420069	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35221086	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35453961	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758603	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752255	0.88[ASN][1000 genomes]
rs4752256	0.87[ASN][1000 genomes]
rs4752322	0.88[ASN][1000 genomes]
rs4752347	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55671354	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55759483	0.88[ASN][1000 genomes]
rs58587374	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61596353	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61867965	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61868024	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6585300	0.89[ASN][1000 genomes]
rs7077148	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079877	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7081975	0.82[ASN][1000 genomes]
rs7082836	0.86[ASN][1000 genomes]
rs7093686	0.89[ASN][1000 genomes]
rs7095816	0.88[ASN][1000 genomes]
rs758585	0.88[ASN][1000 genomes]
rs765173	0.88[ASN][1000 genomes]
rs765174	0.97[ASN][1000 genomes]
rs7895830	0.88[ASN][1000 genomes]
rs7897937	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7898347	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7903663	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7904188	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7907837	0.88[ASN][1000 genomes]
rs7908665	0.88[ASN][1000 genomes]
rs7914792	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7915943	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7918129	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919649	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7920216	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7923693	0.87[ASN][1000 genomes]
rs8181444	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11196959	FAM160B1	cis	Esophagus Muscularis	GTEx
rs11196959	FAM160B1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116589600-116640600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:116611600-116641000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:116617400-116640600	Weak transcription	Fetal Intestine Small	intestine
4	chr10:116619400-116641600	Weak transcription	Aorta	Aorta
5	chr10:116635200-116640600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr10:116636800-116641800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:116637000-116640400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:116637000-116640400	Weak transcription	Colon Smooth Muscle	Colon
9	chr10:116637000-116641200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:116637000-116641400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:116637000-116641400	Weak transcription	Stomach Mucosa	stomach
12	chr10:116637000-116641400	Weak transcription	HSMMtube	muscle
13	chr10:116637000-116641600	Weak transcription	NHEK	skin
14	chr10:116637000-116641800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:116637000-116641800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:116637000-116641800	Weak transcription	NH-A	brain
17	chr10:116637000-116642200	Weak transcription	HMEC	breast
18	chr10:116638600-116641600	Weak transcription	Right Atrium	heart
19	chr10:116638800-116640600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr10:116638800-116641400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr10:116639000-116642000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr10:116639000-116643000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr10:116639200-116640200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr10:116639200-116640800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr10:116639200-116642200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr10:116639200-116642800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr10:116639400-116640600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr10:116639400-116641400	Enhancers	Brain Hippocampus Middle	brain
29	chr10:116639400-116642000	Enhancers	Fetal Kidney	kidney
30	chr10:116639400-116642000	Enhancers	Fetal Muscle Trunk	muscle
31	chr10:116639400-116642200	Enhancers	Fetal Stomach	stomach
32	chr10:116639600-116640600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr10:116639600-116640600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr10:116639600-116641000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:116639600-116641000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr10:116639600-116642000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr10:116639600-116642000	Enhancers	Fetal Intestine Large	intestine
38	chr10:116639600-116642200	Enhancers	H1 Cell Line	embryonic stem cell
39	chr10:116639600-116642200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr10:116639600-116642400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr10:116639800-116640400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr10:116639800-116640400	Enhancers	Brain Anterior Caudate	brain
43	chr10:116639800-116640600	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr10:116639800-116640600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr10:116639800-116641000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr10:116639800-116641400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr10:116639800-116642000	Enhancers	Fetal Lung	lung
48	chr10:116639800-116642200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr10:116639800-116642200	Enhancers	Placenta	Placenta
50	chr10:116639800-116642200	Enhancers	Ovary	ovary

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