Variant report

Variant	rs3024815
Chromosome Location	chr2:85888293-85888294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85884543..85886105-chr2:85886734..85889252,2	MCF-7	breast:
2	chr2:85886964..85889940-chr2:85892432..85895474,3	K562	blood:
3	chr2:85886384..85888298-chr2:85898868..85900454,2	MCF-7	breast:
4	chr2:85886740..85890485-chr2:85890962..85895474,8	K562	blood:
5	chr2:85886996..85889867-chr2:85891019..85894482,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168878	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs3024803	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3024805	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3024810	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3024811	1.00[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3024818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3024819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3024822	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3024827	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3024828	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57175088	0.87[AMR][1000 genomes]
rs57762218	1.00[AMR][1000 genomes]
rs57789237	0.87[AMR][1000 genomes]
rs59048598	1.00[AMR][1000 genomes]
rs59227664	1.00[AMR][1000 genomes]
rs60661938	1.00[AMR][1000 genomes]
rs60755293	1.00[AMR][1000 genomes]
rs60801683	1.00[AMR][1000 genomes]
rs61535370	1.00[AMR][1000 genomes]
rs61536745	1.00[AMR][1000 genomes]
rs6718028	1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[AMR][1000 genomes]
rs72923039	1.00[AMR][1000 genomes]
rs72923051	1.00[AMR][1000 genomes]
rs72923062	1.00[AMR][1000 genomes]
rs72923064	1.00[AMR][1000 genomes]
rs72923077	1.00[AMR][1000 genomes]
rs72923080	1.00[AMR][1000 genomes]
rs72923082	1.00[AMR][1000 genomes]
rs7564769	1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[AMR][1000 genomes]
rs7579847	1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[AMR][1000 genomes]
rs7580358	0.87[AMR][1000 genomes]
rs7584055	0.87[AMR][1000 genomes]
rs7589436	0.87[AMR][1000 genomes]
rs7599812	1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv874464	chr2:85886175-85898898	Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85846200-85889400	Strong transcription	Thymus	Thymus
2	chr2:85876400-85888800	Weak transcription	Fetal Heart	heart
3	chr2:85876400-85888800	Weak transcription	Right Atrium	heart
4	chr2:85876600-85895400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:85877000-85889000	Weak transcription	Stomach Mucosa	stomach
6	chr2:85877000-85890000	Weak transcription	Ovary	ovary
7	chr2:85877200-85888600	Weak transcription	Aorta	Aorta
8	chr2:85877200-85893200	Weak transcription	Brain Substantia Nigra	brain
9	chr2:85877800-85890200	Weak transcription	Small Intestine	intestine
10	chr2:85878200-85888800	Weak transcription	Brain Anterior Caudate	brain
11	chr2:85878800-85891400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:85879400-85889200	Weak transcription	Colonic Mucosa	Colon
13	chr2:85879400-85890200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:85879400-85890200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:85879600-85889800	Weak transcription	Fetal Intestine Large	intestine
16	chr2:85879600-85894000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:85879600-85896000	Weak transcription	GM12878-XiMat	blood
18	chr2:85879800-85888600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:85880200-85888800	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:85880400-85891800	Weak transcription	HepG2	liver
21	chr2:85880600-85888800	Weak transcription	Left Ventricle	heart
22	chr2:85880600-85889400	Weak transcription	Pancreas	Pancrea
23	chr2:85880600-85889600	Weak transcription	Brain Germinal Matrix	brain
24	chr2:85880600-85890200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:85880600-85890200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:85880800-85889800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:85880800-85890200	Weak transcription	K562	blood
28	chr2:85881400-85889200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:85881400-85891000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:85881600-85888800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:85881600-85890200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:85881800-85895800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:85882400-85890400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:85883600-85888400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:85883600-85889000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:85883600-85889400	Weak transcription	Hela-S3	cervix
37	chr2:85883600-85889400	Weak transcription	NHEK	skin
38	chr2:85883600-85890400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:85883600-85892800	Weak transcription	Fetal Lung	lung
40	chr2:85883600-85900000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:85883800-85889400	Weak transcription	NH-A	brain
42	chr2:85883800-85890000	Weak transcription	HMEC	breast
43	chr2:85883800-85890200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:85883800-85890200	Weak transcription	HSMM	muscle
45	chr2:85884000-85889400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:85884000-85889400	Weak transcription	Osteobl	bone
47	chr2:85884000-85889600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:85884200-85889400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:85884200-85890200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:85884800-85888800	Weak transcription	Dnd41	blood

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