Variant report

Variant	rs1496949
Chromosome Location	chr5:178337776-178337777
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:178337710-178337820	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178322017..178324460-chr5:178337015..178339677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213328	TF binding region
ZFP2	TF binding region
ENSG00000198939	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10035887	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10040956	0.88[CEU][hapmap]
rs10043579	0.97[ASN][1000 genomes]
rs10044051	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10055777	0.96[ASN][1000 genomes]
rs10055826	0.97[ASN][1000 genomes]
rs10067521	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10071186	0.93[ASN][1000 genomes]
rs10434800	0.85[ASN][1000 genomes]
rs1046726	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10479515	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10479516	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10516151	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11249601	0.97[ASN][1000 genomes]
rs11249603	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11743869	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11745403	0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11746382	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11955586	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs11960446	0.81[EUR][1000 genomes]
rs12653764	0.85[ASN][1000 genomes]
rs13154558	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13362387	0.90[JPT][hapmap]
rs1496950	1.00[CEU][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995079	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2004503	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4130052	0.88[CEU][hapmap]
rs4700927	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62393052	0.88[EUR][1000 genomes]
rs6600990	0.83[EUR][1000 genomes]
rs6600993	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6600994	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6866021	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6872605	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6872794	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6873993	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6880072	0.97[ASN][1000 genomes]
rs6897783	0.97[ASN][1000 genomes]
rs6898923	0.97[ASN][1000 genomes]
rs6899251	0.97[ASN][1000 genomes]
rs7701607	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7702879	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7718717	0.85[ASN][1000 genomes]
rs953740	0.83[AMR][1000 genomes];0.97[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	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3470830	chr5:178334452-178339256	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3470831	chr5:178334452-178339256	Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178335600-178340600	ZNF genes & repeats	Brain Substantia Nigra	brain
2	chr5:178335600-178349000	ZNF genes & repeats	Liver	Liver
3	chr5:178335800-178337800	ZNF genes & repeats	Gastric	stomach
4	chr5:178335800-178337800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
5	chr5:178335800-178342200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr5:178335800-178367000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr5:178336000-178337800	ZNF genes & repeats	Brain Hippocampus Middle	brain
8	chr5:178336000-178338000	ZNF genes & repeats	Ovary	ovary
9	chr5:178336000-178340400	ZNF genes & repeats	Adipose Nuclei	Adipose
10	chr5:178336200-178337800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:178336200-178337800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
12	chr5:178336200-178337800	ZNF genes & repeats	Fetal Lung	lung
13	chr5:178336200-178338000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
14	chr5:178336200-178338000	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:178336400-178337800	ZNF genes & repeats	Aorta	Aorta
16	chr5:178336400-178337800	ZNF genes & repeats	Spleen	Spleen
17	chr5:178336600-178337800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr5:178336800-178337800	ZNF genes & repeats	Fetal Stomach	stomach
19	chr5:178336800-178338000	ZNF genes & repeats	Esophagus	oesophagus
20	chr5:178336800-178340000	Weak transcription	Fetal Kidney	kidney
21	chr5:178337000-178338000	ZNF genes & repeats	Brain Germinal Matrix	brain
22	chr5:178337000-178340600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:178337400-178337800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr5:178337400-178337800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle

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