Variant report

Variant	rs71417225
Chromosome Location	chr2:153294814-153294815
allele	C/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:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12989510	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13003885	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13009223	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13011684	1.00[EUR][1000 genomes]
rs13026712	1.00[EUR][1000 genomes]
rs13029667	0.80[AFR][1000 genomes]
rs13033209	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13034458	0.80[AFR][1000 genomes]
rs34416306	0.80[AFR][1000 genomes]
rs35191034	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71417226	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	chr2:153290200-153300400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:153290400-153296000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:153290800-153296200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:153291200-153295200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:153291200-153296600	Weak transcription	Adipose Nuclei	Adipose
14	chr2:153291200-153300600	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:153291600-153296200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:153291600-153296600	Weak transcription	Placenta	Placenta
17	chr2:153291600-153300000	Weak transcription	Right Atrium	heart
18	chr2:153291600-153305200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:153291800-153300000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:153292800-153297200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr2:153292800-153298000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:153293000-153295400	Enhancers	H1 Cell Line	embryonic stem cell
23	chr2:153293000-153297400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr2:153293200-153295200	Enhancers	Brain Angular Gyrus	brain
25	chr2:153293200-153296400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:153293200-153297400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr2:153293400-153295400	Enhancers	Psoas Muscle	Psoas
28	chr2:153293400-153297000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:153293600-153296000	Enhancers	Fetal Brain Male	brain
30	chr2:153293600-153297200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr2:153293600-153302400	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr2:153293800-153295400	Enhancers	Fetal Brain Female	brain
33	chr2:153293800-153295400	Enhancers	Fetal Stomach	stomach
34	chr2:153293800-153295800	Enhancers	Fetal Lung	lung
35	chr2:153293800-153297000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:153294000-153295000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr2:153294000-153295600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:153294000-153295800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:153294000-153297000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:153294200-153295200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr2:153294200-153297000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr2:153294200-153298400	Weak transcription	GM12878-XiMat	blood
43	chr2:153294600-153295200	Enhancers	HepG2	liver
44	chr2:153294600-153297000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:153294600-153297000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:153294600-153297600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:153294600-153300600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:153294800-153295400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:153294800-153295400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:153294800-153295400	Enhancers	Fetal Muscle Leg	muscle

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