Variant report

Variant	rs2888599
Chromosome Location	chr7:87229025-87229026
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	chr7:87227402..87230284-chr7:87256828..87258486,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105784	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1015415	1.00[CEU][hapmap]
rs10486996	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487002	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154319	1.00[ASN][1000 genomes]
rs17250003	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17327747	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17328198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17328260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17328288	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17328447	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17328880	1.00[CEU][hapmap]
rs17329661	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17329751	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17330078	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008850	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078998	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2188522	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2188525	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2188528	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2188532	1.00[CEU][hapmap]
rs2214103	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2235024	1.00[ASN][1000 genomes]
rs2235074	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs28381718	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28381767	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28381770	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28381780	1.00[CEU][hapmap]
rs28381787	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28381797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28381877	1.00[ASN][1000 genomes]
rs28381910	1.00[ASN][1000 genomes]
rs28746504	0.94[EUR][1000 genomes]
rs3213619	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs45443201	1.00[ASN][1000 genomes]
rs57392086	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58448193	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58733016	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61216993	0.82[EUR][1000 genomes]
rs7779492	1.00[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	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1026153	chr7:86905796-87258822	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87226800-87230600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr7:87227400-87229200	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr7:87227400-87230800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:87227600-87229600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:87227600-87230200	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr7:87227800-87229400	Active TSS	Primary T cells fromperipheralblood	blood
7	chr7:87227800-87229400	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr7:87227800-87229400	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr7:87227800-87230400	Active TSS	Rectal Smooth Muscle	rectum
10	chr7:87227800-87230800	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr7:87228000-87229400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:87228400-87229800	Active TSS	HepG2	liver
13	chr7:87228400-87230400	Active TSS	Liver	Liver
14	chr7:87228600-87229400	Active TSS	Placenta	Placenta
15	chr7:87228600-87229600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr7:87228600-87230200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr7:87228600-87230600	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr7:87228600-87230600	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr7:87228600-87230600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:87228800-87229200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:87228800-87229400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:87228800-87229400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr7:87228800-87229400	Active TSS	Brain Cingulate Gyrus	brain
24	chr7:87228800-87229400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr7:87228800-87229600	Active TSS	Brain Hippocampus Middle	brain
26	chr7:87228800-87229600	Active TSS	Colonic Mucosa	Colon
27	chr7:87228800-87229600	Enhancers	Pancreas	Pancrea
28	chr7:87228800-87229600	Active TSS	Small Intestine	intestine
29	chr7:87228800-87230200	Active TSS	Brain Anterior Caudate	brain
30	chr7:87228800-87230200	Active TSS	Ovary	ovary
31	chr7:87228800-87230400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr7:87228800-87230600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
33	chr7:87229000-87229200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr7:87229000-87229200	Bivalent/Poised TSS	Thymus	Thymus
35	chr7:87229000-87229400	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr7:87229000-87229400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:87229000-87229400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:87229000-87229400	Active TSS	Fetal Intestine Large	intestine
39	chr7:87229000-87229400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
40	chr7:87229000-87229400	Enhancers	GM12878-XiMat	blood
41	chr7:87229000-87230000	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr7:87229000-87230200	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr7:87229000-87230400	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr7:87229000-87230400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:87229000-87230400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
46	chr7:87229000-87230600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr7:87229000-87230600	Active TSS	Brain Angular Gyrus	brain

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