Variant report

Variant	rs6787901
Chromosome Location	chr3:85938439-85938440
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10084716	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11711972	0.88[CEU][hapmap]
rs11715949	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494511	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12636273	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs12714642	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13068185	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13085195	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13325188	0.85[YRI][hapmap]
rs1375218	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs1375219	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1448607	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs1448616	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1562626	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2044654	0.86[JPT][hapmap]
rs2324937	0.92[CEU][hapmap]
rs2324938	0.92[CEU][hapmap]
rs2324939	0.93[CEU][hapmap]
rs2324981	0.92[CEU][hapmap]
rs2325005	0.93[CEU][hapmap]
rs2325036	0.82[JPT][hapmap]
rs2325037	0.80[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3901898	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs3906942	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3930071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4129497	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234702	0.92[CEU][hapmap]
rs4302393	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302394	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4308293	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4364177	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4488844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4555536	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs4555539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4688896	0.92[CEU][hapmap]
rs4856279	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs4856606	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4856607	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56282418	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6549053	0.84[CEU][hapmap]
rs6549054	0.82[JPT][hapmap]
rs6549055	0.81[CHB][hapmap]
rs6549061	0.89[ASN][1000 genomes]
rs6549063	0.91[EUR][1000 genomes]
rs6769012	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6782553	0.85[EUR][1000 genomes]
rs6796380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799453	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7426412	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7609709	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7611409	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7612371	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs7614073	0.92[EUR][1000 genomes]
rs7620544	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621146	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap]
rs7622132	0.84[YRI][hapmap]
rs7623735	0.93[CEU][hapmap]
rs7625223	0.93[CEU][hapmap]
rs7626873	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7630752	0.93[CEU][hapmap]
rs7632162	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7634560	0.92[CEU][hapmap]
rs7636187	0.86[YRI][hapmap]
rs7636206	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7637221	0.93[CEU][hapmap];0.91[JPT][hapmap]
rs7638774	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs7640041	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs7642281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7648895	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7653470	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs9309992	0.85[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9309996	0.92[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9310000	0.85[EUR][1000 genomes]
rs9681744	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs9713674	0.92[EUR][1000 genomes]
rs9810861	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs9824085	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs9824980	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9829446	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9832847	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836755	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9841158	0.80[EUR][1000 genomes]
rs9843797	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9846878	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9850482	0.86[CEU][hapmap];0.93[EUR][1000 genomes]
rs9851502	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9864042	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9866273	0.93[CEU][hapmap]
rs9875386	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs9876664	0.82[JPT][hapmap]
rs9881886	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs9985228	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv877108	chr3:85870363-86037162	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv877109	chr3:85892098-86006210	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv877110	chr3:85892098-86037162	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv877111	chr3:85892098-86044224	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
8	nsv460754	chr3:85917289-86006210	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv460755	chr3:85917289-86006210	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv590912	chr3:85917289-86006210	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
11	nsv470727	chr3:85917289-86044224	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
12	nsv590913	chr3:85917289-86044224	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85935400-85939200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:85937800-85940000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr3:85937800-85940400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:85938000-85939400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:85938200-85939000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:85938400-85940000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:85938400-85940200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:85938400-85940600	Enhancers	H1 Cell Line	embryonic stem cell

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