Variant report

Variant	rs28420171
Chromosome Location	chr2:134256199-134256200
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:134250533..134253276-chr2:134255115..134256615,2	MCF-7	breast:
2	chr2:134253868..134259578-chr2:134259579..134266138,12	MCF-7	breast:
3	chr2:134251643..134253707-chr2:134255624..134257629,2	MCF-7	breast:
4	chr2:134248085..134250298-chr2:134253580..134256578,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10172908	1.00[EUR][1000 genomes]
rs10176630	1.00[EUR][1000 genomes]
rs10179509	1.00[EUR][1000 genomes]
rs10180776	1.00[EUR][1000 genomes]
rs10182352	1.00[EUR][1000 genomes]
rs10204302	1.00[EUR][1000 genomes]
rs11904353	1.00[EUR][1000 genomes]
rs13383175	1.00[EUR][1000 genomes]
rs13383603	1.00[EUR][1000 genomes]
rs13396221	1.00[EUR][1000 genomes]
rs13402934	1.00[EUR][1000 genomes]
rs13406195	1.00[EUR][1000 genomes]
rs13406470	1.00[EUR][1000 genomes]
rs13410388	1.00[EUR][1000 genomes]
rs13419194	1.00[EUR][1000 genomes]
rs13432659	1.00[EUR][1000 genomes]
rs1897430	1.00[EUR][1000 genomes]
rs1897431	1.00[EUR][1000 genomes]
rs28634361	1.00[EUR][1000 genomes]
rs6718180	1.00[EUR][1000 genomes]
rs6727895	1.00[EUR][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	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134240000-134262400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:134246400-134262400	Weak transcription	Gastric	stomach
3	chr2:134248000-134262000	Weak transcription	NHLF	lung
4	chr2:134248200-134256600	Weak transcription	NHEK	skin
5	chr2:134250200-134257200	Enhancers	Fetal Intestine Small	intestine
6	chr2:134250800-134257800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:134251600-134261400	Weak transcription	Right Atrium	heart
8	chr2:134252200-134257000	Enhancers	Fetal Kidney	kidney
9	chr2:134252600-134257000	Enhancers	Fetal Brain Female	brain
10	chr2:134252600-134257600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:134254000-134256600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:134254000-134256600	Enhancers	Fetal Lung	lung
13	chr2:134254200-134257600	Enhancers	Fetal Intestine Large	intestine
14	chr2:134254600-134256600	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr2:134254800-134256200	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr2:134254800-134256600	Enhancers	Fetal Stomach	stomach
17	chr2:134254800-134257400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:134255000-134256200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:134255000-134258200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:134255200-134256800	Enhancers	Fetal Brain Male	brain
21	chr2:134255200-134257000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:134255400-134256600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:134255400-134257000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:134255400-134257200	Enhancers	Brain Germinal Matrix	brain
25	chr2:134255400-134259800	Weak transcription	Left Ventricle	heart
26	chr2:134255400-134261800	Weak transcription	Brain Anterior Caudate	brain
27	chr2:134255400-134261800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:134255400-134262000	Weak transcription	Brain Angular Gyrus	brain
29	chr2:134255400-134262200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:134255600-134256200	Enhancers	Duodenum Mucosa	Duodenum
31	chr2:134255600-134256400	Weak transcription	Small Intestine	intestine
32	chr2:134255600-134256400	Weak transcription	Stomach Mucosa	stomach
33	chr2:134255600-134260400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:134255800-134258600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:134255800-134260200	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:134255800-134260400	Weak transcription	Liver	Liver
37	chr2:134255800-134260600	Weak transcription	Brain Substantia Nigra	brain
38	chr2:134256000-134257400	Enhancers	NHDF-Ad	bronchial

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