Variant report

Variant	rs6115009
Chromosome Location	chr20:25020331-25020332
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25017798..25020869-chr20:25030431..25033464,3	MCF-7	breast:
2	chr20:25014177..25016183-chr20:25020010..25021666,2	MCF-7	breast:
3	chr20:25018135..25021325-chr20:25025439..25028774,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs6050267	1.00[ASN][1000 genomes]
rs6076312	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083725	0.93[CEU][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083726	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083727	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083728	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083729	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6115010	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115011	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115013	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217192	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7262168	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7273310	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];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	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25012000-25026400	Enhancers	Right Ventricle	heart
2	chr20:25012800-25026400	Enhancers	Brain Angular Gyrus	brain
3	chr20:25013400-25022600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr20:25014000-25026400	Enhancers	Brain Cingulate Gyrus	brain
5	chr20:25014200-25023000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr20:25014200-25026400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr20:25014400-25025600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr20:25016000-25021200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr20:25016200-25020800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr20:25016200-25021800	Enhancers	Colonic Mucosa	Colon
11	chr20:25016200-25023800	Enhancers	Stomach Mucosa	stomach
12	chr20:25016200-25024200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr20:25016200-25024600	Enhancers	Fetal Thymus	thymus
14	chr20:25016400-25020400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr20:25016400-25020400	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr20:25016400-25020800	Enhancers	Adipose Nuclei	Adipose
17	chr20:25016400-25020800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr20:25016400-25021000	Genic enhancers	Fetal Intestine Large	intestine
19	chr20:25016400-25024000	Enhancers	Small Intestine	intestine
20	chr20:25016400-25024400	Genic enhancers	Fetal Intestine Small	intestine
21	chr20:25016400-25025800	Enhancers	Fetal Heart	heart
22	chr20:25016600-25021400	Enhancers	Fetal Lung	lung
23	chr20:25016600-25021600	Enhancers	Ovary	ovary
24	chr20:25016600-25022200	Genic enhancers	Fetal Stomach	stomach
25	chr20:25016600-25023800	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr20:25016600-25024600	Enhancers	Pancreas	Pancrea
27	chr20:25016600-25025400	Enhancers	Fetal Muscle Leg	muscle
28	chr20:25016600-25027600	Enhancers	Right Atrium	heart
29	chr20:25016600-25034800	Weak transcription	A549	lung
30	chr20:25016800-25021200	Enhancers	Spleen	Spleen
31	chr20:25017000-25020800	Enhancers	Fetal Brain Male	brain
32	chr20:25017000-25022000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr20:25017000-25022000	Enhancers	Brain Hippocampus Middle	brain
34	chr20:25017000-25026600	Enhancers	Brain Anterior Caudate	brain
35	chr20:25017400-25020400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr20:25017400-25021400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr20:25017400-25026400	Enhancers	Brain Substantia Nigra	brain
38	chr20:25017600-25026400	Enhancers	Left Ventricle	heart
39	chr20:25017800-25020800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr20:25017800-25021200	Enhancers	NHDF-Ad	bronchial
41	chr20:25017800-25021400	Enhancers	Gastric	stomach
42	chr20:25017800-25022400	Enhancers	Esophagus	oesophagus
43	chr20:25017800-25023400	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr20:25017800-25024400	Enhancers	Lung	lung
45	chr20:25017800-25029000	Genic enhancers	Placenta	Placenta
46	chr20:25017800-25034200	Weak transcription	Fetal Kidney	kidney
47	chr20:25018000-25021000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr20:25018000-25022600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr20:25018200-25020400	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr20:25018200-25021400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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