Variant report

Variant	rs72809310
Chromosome Location	chr10:90647992-90647993
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90640427..90642402-chr10:90647298..90648945,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138134	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1008719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10887870	0.84[EUR][1000 genomes]
rs11202897	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11202898	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202899	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202901	0.80[AMR][1000 genomes]
rs11202902	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202906	0.83[EUR][1000 genomes]
rs11591231	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11596205	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1214564	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12241401	0.98[EUR][1000 genomes]
rs12254856	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12267680	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17114327	0.82[EUR][1000 genomes]
rs2119685	0.83[EUR][1000 genomes]
rs2439707	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2481918	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41284106	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41317244	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45493098	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56104559	0.99[EUR][1000 genomes]
rs56228317	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56268252	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57807025	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59737591	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66478243	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7078383	0.82[EUR][1000 genomes]
rs7085698	0.84[EUR][1000 genomes]
rs7090631	0.84[EUR][1000 genomes]
rs7098235	0.84[EUR][1000 genomes]
rs72809311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809314	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809318	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809335	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72809337	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72809342	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7897521	0.82[EUR][1000 genomes]
rs7915393	0.83[EUR][1000 genomes]
rs988584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][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	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90641000-90653600	Weak transcription	Gastric	stomach
2	chr10:90641400-90658600	Weak transcription	Brain Angular Gyrus	brain
3	chr10:90641600-90653200	Weak transcription	Colonic Mucosa	Colon
4	chr10:90641800-90653800	Weak transcription	Stomach Mucosa	stomach
5	chr10:90641800-90656400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:90641800-90661800	Weak transcription	Thymus	Thymus
7	chr10:90642000-90648800	Enhancers	Primary B cells from peripheral blood	blood
8	chr10:90642000-90650400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr10:90642000-90651000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr10:90642200-90648000	Weak transcription	Fetal Muscle Leg	muscle
13	chr10:90642200-90648400	Enhancers	Primary T cells from cord blood	blood
14	chr10:90642200-90648800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr10:90642200-90649800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:90642200-90656600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:90642400-90648200	Weak transcription	Adipose Nuclei	Adipose
18	chr10:90642400-90651200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr10:90642400-90652000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:90642600-90648000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr10:90642600-90649200	Weak transcription	Primary B cells from cord blood	blood
22	chr10:90642600-90653800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr10:90642800-90656400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr10:90643200-90651800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr10:90643400-90650400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:90643400-90651800	Weak transcription	NH-A	brain
27	chr10:90643600-90648000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr10:90643600-90648400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:90643600-90650800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr10:90643800-90648000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:90643800-90650000	Enhancers	A549	lung
32	chr10:90643800-90650200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr10:90644200-90652000	Weak transcription	HMEC	breast
34	chr10:90644200-90653400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr10:90644400-90652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:90644600-90648400	Enhancers	Hela-S3	cervix
37	chr10:90644600-90652000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr10:90646000-90648400	Enhancers	Primary T cells fromperipheralblood	blood
39	chr10:90646200-90648600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr10:90646200-90648800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr10:90646400-90648400	Enhancers	Fetal Intestine Large	intestine
42	chr10:90646400-90648400	Enhancers	Small Intestine	intestine
43	chr10:90646400-90648600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr10:90646800-90648000	Flanking Active TSS	GM12878-XiMat	blood
45	chr10:90646800-90650400	Weak transcription	HSMM	muscle
46	chr10:90646800-90651800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr10:90646800-90651800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr10:90646800-90651800	Weak transcription	HSMMtube	muscle
49	chr10:90646800-90651800	Weak transcription	NHEK	skin
50	chr10:90646800-90653600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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