Variant report

Variant	rs6545169
Chromosome Location	chr2:50659031-50659032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10182151	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10191436	0.84[CEU][hapmap]
rs10194754	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10865246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11125300	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs11125301	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11125304	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12465806	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12472592	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12622261	0.84[CEU][hapmap]
rs13382330	0.92[CEU][hapmap]
rs13394447	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1402122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1402129	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs1402167	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs1520435	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1520450	0.81[CEU][hapmap]
rs1520452	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1829534	0.88[CEU][hapmap]
rs1851013	0.96[CEU][hapmap]
rs1851014	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1879319	0.82[JPT][hapmap]
rs1915174	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1949569	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1996669	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2037387	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2139628	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2160444	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35125023	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4031833	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4318425	0.88[CEU][hapmap]
rs4971669	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4971675	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545167	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6545170	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6721052	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6728741	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6736016	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6739297	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7559624	0.81[CEU][hapmap]
rs7574552	0.84[CEU][hapmap]
rs7577661	0.84[CEU][hapmap]
rs7587241	0.91[CEU][hapmap]
rs7607203	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs939399	0.96[CEU][hapmap]
rs939400	0.96[CEU][hapmap]
rs985919	1.00[JPT][hapmap]
rs9917332	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[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	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948548	chr2:50569117-50695100	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv933786	chr2:50628354-50780185	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1010510	chr2:50649641-51011565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv535694	chr2:50649641-51011565	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50658800-50659400	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr2:50659000-50660000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:50659000-50660200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:50659000-50660200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:50659000-50660400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr2:50659000-50660400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr2:50659000-50660400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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