Variant report

Variant	rs765461
Chromosome Location	chr3:85071640-85071641
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1016305	0.85[CHB][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap]
rs1016306	0.85[CHB][hapmap]
rs11927760	0.85[ASN][1000 genomes]
rs1248858	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.91[ASN][1000 genomes]
rs1248859	0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.91[ASN][1000 genomes]
rs1248860	0.85[CHB][hapmap]
rs1248861	0.82[ASN][1000 genomes]
rs13072305	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13081745	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1694977	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1872553	0.90[CHB][hapmap]
rs1872556	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1994315	0.84[CEU][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2035561	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.92[ASN][1000 genomes]
rs2035562	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs2062431	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2200461	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2220243	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2326123	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2326126	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4301023	0.90[CHB][hapmap]
rs4499618	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4569672	0.92[ASN][1000 genomes]
rs4856559	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4856560	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56808719	0.85[ASN][1000 genomes]
rs653481	0.82[ASN][1000 genomes]
rs6549007	1.00[ASW][hapmap]
rs6549009	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6768559	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7645952	0.95[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7647649	0.84[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7651996	0.90[CHB][hapmap]
rs9814390	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9831123	0.90[CHB][hapmap]
rs9855054	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9869902	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.89[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	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
3	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
4	nsv492289	chr3:85066623-85319147	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85055800-85081400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:85065200-85082200	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:85068600-85090600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:85070000-85073000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:85070600-85072800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:85070600-85073000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:85071000-85073400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:85071200-85071800	Enhancers	Brain Angular Gyrus	brain
9	chr3:85071400-85071800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:85071400-85071800	Enhancers	Brain Anterior Caudate	brain
11	chr3:85071400-85071800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr3:85071400-85082400	Weak transcription	Fetal Brain Female	brain
13	chr3:85071600-85071800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:85071600-85073000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:85071600-85074400	Weak transcription	Brain Substantia Nigra	brain
16	chr3:85071600-85082000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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