Variant report

Variant	rs55899933
Chromosome Location	chr5:108351404-108351405
allele	G/T
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	chr5:108351088-108351469	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
RNU6-47P	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10043207	0.87[EUR][1000 genomes]
rs10061582	0.83[ASN][1000 genomes]
rs10447249	0.85[EUR][1000 genomes]
rs11948270	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11948684	0.88[EUR][1000 genomes]
rs11950165	0.85[EUR][1000 genomes]
rs11951285	0.91[EUR][1000 genomes]
rs11951595	0.90[EUR][1000 genomes]
rs11955924	0.91[EUR][1000 genomes]
rs11956572	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11956900	0.86[EUR][1000 genomes]
rs11958129	0.91[EUR][1000 genomes]
rs11960268	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11960336	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11960400	0.90[EUR][1000 genomes]
rs12153527	0.90[EUR][1000 genomes]
rs12153646	0.90[EUR][1000 genomes]
rs12188521	0.88[EUR][1000 genomes]
rs17534347	0.88[EUR][1000 genomes]
rs17534396	0.88[EUR][1000 genomes]
rs3797823	0.83[EUR][1000 genomes]
rs3797825	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3797827	0.88[EUR][1000 genomes]
rs3797830	0.88[EUR][1000 genomes]
rs3822684	0.89[EUR][1000 genomes]
rs4404726	0.80[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56382548	0.91[EUR][1000 genomes]
rs57221554	0.91[EUR][1000 genomes]
rs57814250	0.95[EUR][1000 genomes]
rs58255942	0.87[EUR][1000 genomes]
rs58499805	0.91[EUR][1000 genomes]
rs58729959	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs59409290	0.88[EUR][1000 genomes]
rs60584949	0.91[EUR][1000 genomes]
rs60834821	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66623856	0.91[EUR][1000 genomes]
rs66851282	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs67586696	0.87[EUR][1000 genomes]
rs6861439	0.84[ASN][1000 genomes]
rs6867147	0.86[EUR][1000 genomes]
rs6872299	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6893501	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6893984	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72789336	0.86[EUR][1000 genomes]
rs72789338	0.86[EUR][1000 genomes]
rs72789339	0.86[EUR][1000 genomes]
rs72790513	0.86[EUR][1000 genomes]
rs72790518	0.90[EUR][1000 genomes]
rs72790537	0.91[EUR][1000 genomes]
rs72790543	0.91[EUR][1000 genomes]
rs72790544	0.91[EUR][1000 genomes]
rs72790554	0.90[EUR][1000 genomes]
rs72790558	0.90[EUR][1000 genomes]
rs72790564	0.90[EUR][1000 genomes]
rs72790569	0.81[EUR][1000 genomes]
rs72790570	0.81[EUR][1000 genomes]
rs72790571	0.88[EUR][1000 genomes]
rs72790572	0.88[EUR][1000 genomes]
rs72793921	0.88[EUR][1000 genomes]
rs73778371	0.86[EUR][1000 genomes]
rs73778394	0.91[EUR][1000 genomes]
rs73779112	0.88[EUR][1000 genomes]
rs73780406	0.90[EUR][1000 genomes]
rs73781924	0.90[EUR][1000 genomes]
rs7723942	0.90[EUR][1000 genomes]
rs7725708	0.88[EUR][1000 genomes]
rs7726922	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7731221	0.85[EUR][1000 genomes]
rs7732335	0.90[EUR][1000 genomes]
rs7732510	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016343	chr5:108220116-108364687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv882691	chr5:108229760-108366473	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv4952	chr5:108324146-108369353	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv830443	chr5:108326491-108496723	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108301600-108361200	Weak transcription	Primary T cells from cord blood	blood
2	chr5:108329600-108359600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:108330200-108351800	Weak transcription	Fetal Lung	lung
4	chr5:108332600-108359400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:108332800-108359800	Weak transcription	Adipose Nuclei	Adipose
6	chr5:108333400-108351600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:108341000-108360000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:108341200-108359800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:108341800-108359400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:108342200-108359800	Weak transcription	NHEK	skin
11	chr5:108346400-108359800	Weak transcription	Left Ventricle	heart
12	chr5:108349800-108357600	Weak transcription	Aorta	Aorta
13	chr5:108350400-108359800	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:108350600-108352800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:108350800-108390400	Weak transcription	HSMMtube	muscle
16	chr5:108351400-108352000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr5:108351400-108352200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:108351400-108352800	Enhancers	Ovary	ovary
19	chr5:108351400-108353000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr5:108351400-108359800	Weak transcription	Pancreas	Pancrea

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