Variant report

Variant	rs4408901
Chromosome Location	chr3:99458742-99458743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10935921	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12107242	0.93[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485299	0.85[JPT][hapmap]
rs12486703	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12486901	0.85[JPT][hapmap]
rs12494720	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080329	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13088056	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13088851	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13099452	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1492343	0.85[JPT][hapmap]
rs1871847	0.84[JPT][hapmap]
rs1971381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28820982	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34218799	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34303842	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34906671	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35495890	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35577846	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3921767	0.85[JPT][hapmap]
rs4928143	0.85[JPT][hapmap]
rs4928144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4928219	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928220	0.85[JPT][hapmap]
rs4928222	0.85[JPT][hapmap]
rs55648906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440807	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6800456	0.85[JPT][hapmap]
rs73152013	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613580	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7614366	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7632327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv508231	chr3:99442020-99498951	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99440400-99471000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:99441400-99466800	Weak transcription	NH-A	brain
3	chr3:99443400-99471400	Weak transcription	Aorta	Aorta
4	chr3:99449600-99463400	Weak transcription	HUVEC	blood vessel
5	chr3:99450400-99463600	Weak transcription	NHDF-Ad	bronchial
6	chr3:99450400-99463800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:99451000-99460400	Weak transcription	Osteobl	bone
8	chr3:99457400-99459800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:99458000-99459400	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr3:99458000-99459600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:99458600-99460200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:99458600-99461600	Weak transcription	HSMM	muscle
13	chr3:99458600-99466600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:99458600-99466800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:99458600-99470000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:99458600-99470200	Weak transcription	Lung	lung
17	chr3:99458600-99471000	Weak transcription	NHLF	lung
18	chr3:99458600-99471200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:99458600-99472200	Weak transcription	Adipose Nuclei	Adipose

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