Variant report

Variant	rs248315
Chromosome Location	chr5:179421883-179421884
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	chr5:179420546..179422994-chr5:179425092..179427290,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10068039	0.88[ASN][1000 genomes]
rs1102190	0.89[ASN][1000 genomes]
rs173562	0.87[ASN][1000 genomes]
rs185076	0.91[ASN][1000 genomes]
rs193718	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248257	0.87[ASN][1000 genomes]
rs248258	0.86[ASN][1000 genomes]
rs248316	0.91[ASN][1000 genomes]
rs248319	0.91[ASN][1000 genomes]
rs27014	0.87[ASN][1000 genomes]
rs27016	0.86[ASN][1000 genomes]
rs27017	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27019	0.87[ASN][1000 genomes]
rs2937020	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35928331	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs394588	0.91[ASN][1000 genomes]
rs418384	0.89[ASN][1000 genomes]
rs449511	0.91[ASN][1000 genomes]
rs495267	0.81[ASN][1000 genomes]
rs6871596	0.89[ASN][1000 genomes]
rs6884290	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs857181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857182	0.91[ASN][1000 genomes]
rs857183	0.90[ASN][1000 genomes]
rs857184	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs857189	0.91[ASN][1000 genomes]
rs864137	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs864138	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179396600-179461800	Weak transcription	HSMM	muscle
2	chr5:179404600-179439800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:179405200-179428200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:179405200-179429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:179405200-179453400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:179406000-179428600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr5:179406600-179425400	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:179407000-179428200	Weak transcription	Gastric	stomach
9	chr5:179408000-179427800	Weak transcription	Liver	Liver
10	chr5:179408000-179428200	Weak transcription	Left Ventricle	heart
11	chr5:179408200-179428000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr5:179416200-179428600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:179419000-179424600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:179421000-179422200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr5:179421200-179425800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:179421400-179422000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:179421400-179422600	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:179421400-179422800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:179421400-179422800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:179421400-179422800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:179421400-179423000	ZNF genes & repeats	Brain Germinal Matrix	brain
22	chr5:179421400-179423200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
23	chr5:179421400-179423600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
24	chr5:179421400-179423800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:179421400-179424000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
26	chr5:179421400-179424200	ZNF genes & repeats	Fetal Brain Female	brain
27	chr5:179421600-179422000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
28	chr5:179421600-179422000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr5:179421600-179422400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:179421600-179422400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:179421600-179422600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:179421600-179422600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:179421600-179422800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr5:179421600-179422800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:179421600-179422800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:179421600-179423200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
37	chr5:179421600-179423600	ZNF genes & repeats	Brain Hippocampus Middle	brain
38	chr5:179421800-179422000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr5:179421800-179422000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr5:179421800-179422000	ZNF genes & repeats	Ovary	ovary
41	chr5:179421800-179462400	Weak transcription	Rectal Mucosa Donor 31	rectum

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