Variant report

Variant	rs9881886
Chromosome Location	chr3:85814733-85814734
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11127905	0.90[JPT][hapmap]
rs11711972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494196	0.90[JPT][hapmap]
rs1375218	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1375219	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1448607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1448616	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1562626	0.83[CEU][hapmap]
rs17334733	0.90[JPT][hapmap]
rs1839171	0.80[EUR][1000 genomes]
rs2029051	0.90[JPT][hapmap]
rs2029052	0.90[JPT][hapmap]
rs2029053	0.90[JPT][hapmap]
rs2044654	1.00[JPT][hapmap]
rs2325036	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2325037	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3901898	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs3906942	0.81[EUR][1000 genomes]
rs3930071	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs4302392	0.90[JPT][hapmap]
rs4305433	0.80[JPT][hapmap]
rs4364177	0.90[CEU][hapmap]
rs4435654	0.80[JPT][hapmap]
rs4488844	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs4504176	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4555536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4555539	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs4618235	0.89[JPT][hapmap]
rs4688896	0.83[CEU][hapmap]
rs4856279	0.96[CEU][hapmap];0.88[CHB][hapmap]
rs4856606	0.80[CHB][hapmap]
rs6549053	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs6549054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6549055	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6787901	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs6796380	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs6796402	0.92[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap]
rs6799453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7429346	0.82[EUR][1000 genomes]
rs7611409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7612371	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621146	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs7624423	0.90[JPT][hapmap]
rs7637221	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7638774	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7642281	0.87[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7653470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9309992	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9309996	0.82[CEU][hapmap]
rs9681744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9820133	0.90[JPT][hapmap]
rs9820262	0.90[JPT][hapmap]
rs9836755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9843797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9844720	0.89[JPT][hapmap]
rs9864042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9876664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010541	chr3:85505839-85870597	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536625	chr3:85505839-85870597	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1005102	chr3:85729640-85829412	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	nsv532629	chr3:85763873-86608579	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv460753	chr3:85789007-85820416	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv590911	chr3:85789007-85820416	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv877106	chr3:85814620-86006210	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv877107	chr3:85814620-86037162	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85801200-85815000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85814000-85815000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:85814000-85815200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:85814400-85814800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:85814400-85815000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:85814600-85815200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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