Variant report

Variant	rs2555423
Chromosome Location	chr2:64538764-64538765
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	chr2:64277797..64280331-chr2:64538007..64540114,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10187442	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1030407	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1030409	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1030410	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11125996	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11673882	0.86[ASN][1000 genomes]
rs11682772	0.84[ASN][1000 genomes]
rs11883600	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1365474	0.81[ASN][1000 genomes]
rs1365475	0.81[ASN][1000 genomes]
rs1426712	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1974976	0.85[ASN][1000 genomes]
rs2263647	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278184	0.86[ASN][1000 genomes]
rs2555448	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4485554	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4597511	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546064	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546065	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66506765	0.82[ASN][1000 genomes]
rs6714101	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6724171	0.82[ASN][1000 genomes]
rs6737527	0.82[ASN][1000 genomes]
rs6740438	0.82[ASN][1000 genomes]
rs6748843	0.83[ASN][1000 genomes]
rs6758664	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7561343	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7565077	0.83[ASN][1000 genomes]
rs7585084	0.86[ASN][1000 genomes]
rs7601758	0.95[ASN][1000 genomes]
rs7601803	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs890478	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919122	0.81[ASN][1000 genomes]
rs919123	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919124	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919125	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919126	0.86[ASN][1000 genomes]
rs919127	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930020	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][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	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
7	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64526000-64539200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:64531400-64539400	Weak transcription	Esophagus	oesophagus
3	chr2:64537600-64539200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr2:64537600-64540200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:64537600-64540200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:64537600-64540200	Enhancers	Fetal Thymus	thymus
7	chr2:64537600-64540200	Enhancers	HMEC	breast
8	chr2:64537600-64540800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:64537800-64538800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:64537800-64539200	Enhancers	Brain Germinal Matrix	brain
11	chr2:64537800-64539200	Enhancers	Stomach Mucosa	stomach
12	chr2:64537800-64539800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:64537800-64540000	Enhancers	Placenta	Placenta
14	chr2:64537800-64540200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:64537800-64540800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:64537800-64540800	Enhancers	Fetal Muscle Leg	muscle
17	chr2:64537800-64540800	Enhancers	Fetal Stomach	stomach
18	chr2:64538000-64539200	Enhancers	Brain Angular Gyrus	brain
19	chr2:64538000-64539200	Enhancers	Brain Hippocampus Middle	brain
20	chr2:64538000-64539400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr2:64538000-64540000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:64538000-64540200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:64538000-64540200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:64538000-64540600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:64538000-64540600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr2:64538200-64538800	Enhancers	Fetal Brain Female	brain
27	chr2:64538200-64538800	Enhancers	Lung	lung
28	chr2:64538200-64538800	Flanking Bivalent TSS/Enh	HepG2	liver
29	chr2:64538200-64538800	Flanking Active TSS	NHEK	skin
30	chr2:64538200-64539200	Enhancers	Brain Substantia Nigra	brain
31	chr2:64538200-64540200	Enhancers	Fetal Intestine Large	intestine
32	chr2:64538200-64540600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr2:64538200-64540800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr2:64538200-64543800	Enhancers	Fetal Brain Male	brain
35	chr2:64538400-64538800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:64538400-64538800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr2:64538400-64538800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr2:64538400-64538800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr2:64538400-64539000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:64538400-64539000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:64538400-64539400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr2:64538400-64539400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:64538400-64539800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:64538400-64539800	Enhancers	Right Atrium	heart
45	chr2:64538400-64540000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr2:64538400-64540000	Enhancers	Fetal Intestine Small	intestine
47	chr2:64538400-64540000	Enhancers	Pancreas	Pancrea
48	chr2:64538400-64540800	Enhancers	H1 Cell Line	embryonic stem cell
49	chr2:64538400-64540800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:64538600-64539000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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