Variant report

Variant	rs253485
Chromosome Location	chr5:16898653-16898654
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	chr5:16892933..16897070-chr5:16897498..16901971,5	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs16869226	0.82[AFR][1000 genomes]
rs253483	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs253484	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2560842	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2560846	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2560848	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562350	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2562352	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2562353	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2562354	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562356	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2562357	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2625172	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2625174	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2625175	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56997603	0.82[AFR][1000 genomes]
rs60434528	0.82[AFR][1000 genomes]
rs62371016	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6896099	0.84[AFR][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	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1034844	chr5:16854341-16903100	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16893600-16899000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:16894000-16899000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr5:16894200-16898800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:16894400-16900000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:16895000-16903000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:16895600-16902000	Enhancers	Hela-S3	cervix
7	chr5:16896000-16901200	Weak transcription	Spleen	Spleen
8	chr5:16896000-16912400	Weak transcription	Esophagus	oesophagus
9	chr5:16896400-16901200	Weak transcription	Left Ventricle	heart
10	chr5:16897000-16899200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:16897000-16901200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:16897000-16902800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:16897600-16902000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:16897800-16899200	Weak transcription	HMEC	breast
15	chr5:16898000-16900400	Weak transcription	Fetal Brain Male	brain
16	chr5:16898000-16901800	Weak transcription	HSMMtube	muscle
17	chr5:16898000-16902800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:16898000-16902800	Weak transcription	HSMM	muscle
19	chr5:16898200-16899200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:16898200-16899400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:16898200-16899400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:16898200-16899400	Weak transcription	Pancreas	Pancrea
23	chr5:16898200-16899600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:16898200-16900200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:16898200-16900200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:16898200-16900200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:16898200-16900200	Weak transcription	NHDF-Ad	bronchial
28	chr5:16898200-16900400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:16898200-16900400	Weak transcription	Fetal Brain Female	brain
30	chr5:16898200-16900400	Weak transcription	Stomach Mucosa	stomach
31	chr5:16898200-16901200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:16898200-16901200	Weak transcription	Gastric	stomach
33	chr5:16898200-16901200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:16898200-16901400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr5:16898200-16901400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:16898200-16901600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:16898200-16901600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr5:16898200-16902600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:16898200-16902800	Weak transcription	Colon Smooth Muscle	Colon
40	chr5:16898200-16903000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:16898200-16903400	Weak transcription	Placenta	Placenta
42	chr5:16898200-16903800	Weak transcription	Osteobl	bone
43	chr5:16898200-16904000	Weak transcription	NHLF	lung
44	chr5:16898200-16906200	Weak transcription	Psoas Muscle	Psoas
45	chr5:16898200-16912600	Weak transcription	NH-A	brain
46	chr5:16898400-16899200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:16898400-16899400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:16898400-16899400	Weak transcription	HUVEC	blood vessel
49	chr5:16898400-16899600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr5:16898400-16899800	Weak transcription	H9 Cell Line	embryonic stem cell

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