Variant report

Variant	rs1539407
Chromosome Location	chr10:26855327-26855328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:26854569..26856089-chrX:118738967..118740548,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABI1-4	chr10:26854421-26855838	ENSG00000246873
2	lnc-PDSS1-7	chr10:26854425-26855838	NONHSAT011828

Variant related genes	Relation type
ENSG00000186416	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16927137	0.82[AMR][1000 genomes]
rs17669071	0.84[ASN][1000 genomes]
rs787016	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7897115	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv550229	chr10:26848206-26889823	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv971873	chr10:26850516-26870913	Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3332234	chr10:26853285-26881775	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3441332	chr10:26854971-26857519	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3390225	chr10:26855181-26855642	Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3435900	chr10:26855246-26857194	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26834800-26858400	Strong transcription	Dnd41	blood
2	chr10:26839600-26860800	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr10:26839800-26861200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr10:26840000-26860000	Strong transcription	Primary B cells from peripheral blood	blood
5	chr10:26840200-26863200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:26845000-26855600	Weak transcription	Esophagus	oesophagus
7	chr10:26845400-26863000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr10:26846000-26859600	Strong transcription	Primary B cells from cord blood	blood
9	chr10:26846200-26859000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr10:26846400-26860800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr10:26846400-26861600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr10:26846600-26858200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:26846600-26858400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr10:26846600-26859600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr10:26846600-26860800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr10:26846800-26859400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:26846800-26861200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:26846800-26863000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr10:26847600-26857400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:26848200-26861000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr10:26848400-26863000	Strong transcription	Fetal Thymus	thymus
22	chr10:26848600-26855600	Weak transcription	Gastric	stomach
23	chr10:26848800-26855400	Strong transcription	Primary hematopoietic stem cells	blood
24	chr10:26848800-26857800	Strong transcription	Liver	Liver
25	chr10:26849000-26855400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
26	chr10:26849000-26855600	Strong transcription	Adipose Nuclei	Adipose
27	chr10:26849000-26857600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr10:26849000-26859000	Strong transcription	GM12878-XiMat	blood
29	chr10:26849000-26860600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr10:26849200-26855400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr10:26849200-26855400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr10:26849400-26855600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr10:26849400-26855600	Weak transcription	Pancreas	Pancrea
34	chr10:26849600-26855400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr10:26853000-26855600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr10:26853400-26856600	Strong transcription	Spleen	Spleen
37	chr10:26854000-26860800	Strong transcription	Thymus	Thymus
38	chr10:26854600-26855600	Weak transcription	Lung	lung
39	chr10:26854600-26860200	Strong transcription	Primary T cells from cord blood	blood
40	chr10:26854800-26856400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr10:26855000-26859800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:26855200-26855400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr10:26855200-26855600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr10:26855200-26856000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr10:26855200-26856400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr10:26855200-26856800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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