Variant report

Variant	rs6838117
Chromosome Location	chr4:143342213-143342214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1155075	0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs11938760	0.83[JPT][hapmap]
rs13133199	0.85[AMR][1000 genomes]
rs1391095	0.86[CEU][hapmap];0.92[JPT][hapmap]
rs1391097	0.95[CEU][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1497386	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1497388	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17016027	0.92[JPT][hapmap]
rs2029990	0.83[JPT][hapmap]
rs2130253	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2646095	0.84[CEU][hapmap]
rs2840094	0.89[AFR][1000 genomes]
rs3756125	0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs3775707	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4626289	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71608480	0.81[EUR][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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr4:143329000-143350000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:143330200-143344800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:143338600-143344800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:143338600-143348800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:143338600-143366600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:143339000-143355400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:143341000-143342600	Enhancers	HUVEC	blood vessel
8	chr4:143341000-143344800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:143341800-143342400	Enhancers	Stomach Mucosa	stomach

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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