Variant report

Variant	rs6880005
Chromosome Location	chr5:107601285-107601286
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10036675	0.94[CEU][hapmap]
rs10061044	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10515385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10515388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11242664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12652237	0.92[CHB][hapmap]
rs12652460	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap]
rs12652675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12653027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12653689	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12654140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12657542	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12658760	0.80[EUR][1000 genomes]
rs12658885	0.80[EUR][1000 genomes]
rs12659437	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17161193	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17384285	0.83[JPT][hapmap]
rs17385914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17386492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17386875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17387645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17388244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17450705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17451397	0.94[CEU][hapmap]
rs17452357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17452992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2052463	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2193972	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap]
rs2416528	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4129424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4364376	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55755463	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56044682	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56855707	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58131807	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58212758	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58844678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61603913	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6870480	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6888190	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72791270	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73214528	1.00[ASN][1000 genomes]
rs73214536	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7703032	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7703347	0.80[EUR][1000 genomes]
rs7704811	0.80[EUR][1000 genomes]
rs7711717	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7724245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7724860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs888792	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534281	chr5:107357579-107674981	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv830441	chr5:107450392-107614557	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv882684	chr5:107521677-107695558	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv830442	chr5:107539150-107697020	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv882685	chr5:107564746-107695558	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv4950	chr5:107587778-107637348	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv882687	chr5:107595383-107695558	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv882688	chr5:107595383-107715746	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107575400-107617600	Weak transcription	Primary B cells from cord blood	blood
2	chr5:107577000-107616000	Weak transcription	Primary T cells from cord blood	blood
3	chr5:107585000-107617800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:107593600-107614000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:107596400-107601400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:107596400-107602000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:107596600-107616000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:107596800-107602000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr5:107600000-107602600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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