Variant report

Variant	rs250343
Chromosome Location	chr5:16725073-16725074
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	chr5:16723686..16725760-chr5:16727885..16730861,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs152726	0.90[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs153182	0.84[ASN][1000 genomes]
rs153183	0.85[EUR][1000 genomes]
rs153184	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs153185	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs173738	0.89[LWK][hapmap]
rs193924	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs26740	0.84[LWK][hapmap]
rs27552	0.80[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs31290	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs31299	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs31497	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs39887	0.80[AMR][1000 genomes]
rs39889	0.81[ASN][1000 genomes]
rs40979	0.85[ASW][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs42564	0.85[ASW][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869660	chr5:16651289-16766428	Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv880373	chr5:16710572-16785604	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16682400-16736000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:16711200-16736400	Weak transcription	Hela-S3	cervix
3	chr5:16711400-16727800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:16711400-16728200	Weak transcription	Spleen	Spleen
5	chr5:16711400-16730200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:16711400-16731800	Weak transcription	HMEC	breast
7	chr5:16711600-16736000	Weak transcription	Placenta	Placenta
8	chr5:16713800-16731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:16713800-16735600	Weak transcription	Colonic Mucosa	Colon
10	chr5:16714000-16726200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:16714000-16726200	Weak transcription	Left Ventricle	heart
12	chr5:16714000-16730200	Weak transcription	Osteobl	bone
13	chr5:16714200-16726200	Weak transcription	Fetal Kidney	kidney
14	chr5:16714200-16730400	Weak transcription	NHLF	lung
15	chr5:16714200-16736000	Weak transcription	NHDF-Ad	bronchial
16	chr5:16714400-16730000	Weak transcription	NH-A	brain
17	chr5:16714600-16726400	Weak transcription	Brain Substantia Nigra	brain
18	chr5:16714600-16728200	Weak transcription	Psoas Muscle	Psoas
19	chr5:16715000-16725400	Weak transcription	HUVEC	blood vessel
20	chr5:16721400-16725800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:16721600-16725600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:16722000-16726000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:16722200-16730200	Weak transcription	Stomach Mucosa	stomach
24	chr5:16722200-16734200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:16722400-16725600	Weak transcription	HSMM	muscle
26	chr5:16722400-16726000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:16722400-16726200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:16722400-16726200	Weak transcription	HSMMtube	muscle
29	chr5:16722400-16726400	Weak transcription	Gastric	stomach
30	chr5:16722400-16726800	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:16722400-16728000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:16722400-16728000	Weak transcription	Brain Angular Gyrus	brain
33	chr5:16722400-16728000	Weak transcription	Lung	lung
34	chr5:16722400-16728000	Weak transcription	Pancreas	Pancrea
35	chr5:16722400-16728200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:16722400-16729800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:16722400-16730000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr5:16722400-16730000	Weak transcription	NHEK	skin
39	chr5:16722400-16730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:16722400-16734000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:16722600-16726200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:16722600-16726200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:16722600-16726600	Weak transcription	Fetal Brain Female	brain
44	chr5:16722600-16727800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:16722600-16728200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr5:16722600-16736000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr5:16722800-16726200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr5:16722800-16726200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr5:16722800-16726200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr5:16722800-16727800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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