Variant report

Variant	rs9875727
Chromosome Location	chr3:116166214-116166215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10513826	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs13094055	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13316464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16824908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16824913	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1920175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1920197	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35192256	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35220064	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41442746	0.89[CEU][hapmap]
rs4831097	0.89[CEU][hapmap]
rs9289053	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9857124	0.89[CEU][hapmap]
rs9881385	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[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	esv2757886	chr3:116142130-116307542	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2759171	chr3:116142130-116307542	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr3:116164200-116169800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:116165000-116167200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:116165200-116166800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:116165200-116168400	Weak transcription	Fetal Brain Male	brain
5	chr3:116165200-116168600	Weak transcription	Fetal Lung	lung
6	chr3:116165400-116167000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:116165400-116167200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:116165400-116167200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:116165400-116168200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:116165400-116169400	Weak transcription	Brain Angular Gyrus	brain
11	chr3:116165600-116167200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:116165600-116167200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:116165600-116167200	Weak transcription	Brain Substantia Nigra	brain
14	chr3:116165600-116168200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:116165600-116168400	Weak transcription	Brain Anterior Caudate	brain
16	chr3:116165600-116168400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:116165600-116168800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:116165600-116171600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:116166000-116166400	Enhancers	Colon Smooth Muscle	Colon

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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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