Variant report

Variant	rs1872553
Chromosome Location	chr3:85053425-85053426
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1016305	0.84[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1016306	0.80[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1248857	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1248858	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs1248859	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1248860	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13081745	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1694977	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs1872556	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs2035561	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs2035562	0.95[CHB][hapmap]
rs2326123	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs4301023	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4499618	0.81[CHB][hapmap]
rs6768455	0.80[YRI][hapmap];0.86[EUR][1000 genomes]
rs7651996	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765461	0.90[CHB][hapmap]
rs9816652	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9831123	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833081	0.86[EUR][1000 genomes]
rs9834688	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836888	0.86[EUR][1000 genomes]
rs9840607	0.84[ASN][1000 genomes]
rs9871198	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1001316	chr3:84773522-85071342	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv877091	chr3:84876250-85069287	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85041200-85054200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:85048000-85054000	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:85048000-85055200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:85048400-85055000	Weak transcription	Brain Angular Gyrus	brain
5	chr3:85048600-85054200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:85048800-85055200	Weak transcription	Liver	Liver
7	chr3:85048800-85055200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:85048800-85056600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:85052400-85054200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr3:85052600-85054000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:85052800-85054000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:85053000-85054000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:85053200-85054200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:85053200-85055200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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