Variant report

Variant	rs4664109
Chromosome Location	chr2:153294515-153294516
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153276918..153279162-chr2:153293453..153296119,2	MCF-7	breast:
2	chr2:153292111..153294538-chr2:153295389..153297275,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10169514	1.00[CHB][hapmap]
rs10191361	1.00[CHB][hapmap]
rs11684450	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11885624	1.00[JPT][hapmap]
rs12471183	1.00[CHB][hapmap]
rs17399080	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1878632	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs4664583	0.83[CEU][hapmap]
rs56117902	0.82[EUR][1000 genomes]
rs62180799	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6742066	1.00[CHB][hapmap]
rs6759772	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153280000-153305200	Enhancers	Brain Cingulate Gyrus	brain
2	chr2:153282600-153304400	Enhancers	Brain Anterior Caudate	brain
3	chr2:153286200-153301000	Enhancers	Brain Hippocampus Middle	brain
4	chr2:153286400-153305200	Enhancers	Brain Substantia Nigra	brain
5	chr2:153289200-153296800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:153289200-153301800	Weak transcription	NH-A	brain
7	chr2:153289600-153296600	Weak transcription	Small Intestine	intestine
8	chr2:153289600-153301400	Weak transcription	Fetal Thymus	thymus
9	chr2:153290200-153294800	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:153290200-153300400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:153290400-153296000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:153290800-153296200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:153291200-153295200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:153291200-153296600	Weak transcription	Adipose Nuclei	Adipose
15	chr2:153291200-153300600	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:153291600-153294800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:153291600-153296200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:153291600-153296600	Weak transcription	Placenta	Placenta
19	chr2:153291600-153300000	Weak transcription	Right Atrium	heart
20	chr2:153291600-153305200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:153291800-153294600	Weak transcription	HepG2	liver
22	chr2:153291800-153294800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:153291800-153294800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:153291800-153294800	Weak transcription	Ovary	ovary
25	chr2:153291800-153294800	Weak transcription	NHEK	skin
26	chr2:153291800-153300000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:153292800-153297200	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr2:153292800-153298000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr2:153293000-153295400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr2:153293000-153297400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr2:153293200-153295200	Enhancers	Brain Angular Gyrus	brain
32	chr2:153293200-153296400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:153293200-153297400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr2:153293400-153295400	Enhancers	Psoas Muscle	Psoas
35	chr2:153293400-153297000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:153293600-153294800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:153293600-153296000	Enhancers	Fetal Brain Male	brain
38	chr2:153293600-153297200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr2:153293600-153302400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr2:153293800-153294800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:153293800-153295400	Enhancers	Fetal Brain Female	brain
42	chr2:153293800-153295400	Enhancers	Fetal Stomach	stomach
43	chr2:153293800-153295800	Enhancers	Fetal Lung	lung
44	chr2:153293800-153297000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:153294000-153295000	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr2:153294000-153295600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:153294000-153295800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:153294000-153297000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:153294200-153294600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:153294200-153294600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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