Variant report

Variant	rs1475950
Chromosome Location	chr5:178410538-178410539
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10464050	0.85[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1475949	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17078865	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17081834	0.81[EUR][1000 genomes]
rs1826862	0.91[ASW][hapmap];0.89[CHB][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2132673	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56740821	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56773504	0.81[EUR][1000 genomes]
rs56790802	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56954828	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59485557	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59515073	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60629856	0.90[ASN][1000 genomes]
rs60948868	0.88[ASN][1000 genomes]
rs61087919	0.85[ASN][1000 genomes]
rs61213092	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61314110	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867653	0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs6871003	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73334721	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73334723	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73334729	0.86[ASN][1000 genomes]
rs73334737	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73336533	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73336535	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637932	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600489	chr5:178368096-178430375	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1017941	chr5:178384214-178427401	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv537974	chr5:178384214-178427401	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv883219	chr5:178390237-178454118	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv883220	chr5:178394717-178454118	ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv600490	chr5:178405251-178430375	Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv527183	chr5:178409285-178415937	ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv516324	chr5:178410538-178415937	ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv883221	chr5:178410538-178454118	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178369400-178418200	ZNF genes & repeats	Fetal Brain Female	brain
2	chr5:178401000-178414600	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr5:178402000-178414400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr5:178405400-178418200	ZNF genes & repeats	Brain Germinal Matrix	brain
5	chr5:178408000-178411200	ZNF genes & repeats	Pancreas	Pancrea
6	chr5:178408000-178413800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:178409800-178411000	ZNF genes & repeats	Colonic Mucosa	Colon
8	chr5:178409800-178411600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:178409800-178411600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
10	chr5:178409800-178412200	ZNF genes & repeats	Esophagus	oesophagus
11	chr5:178410000-178412200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:178410000-178414600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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