Variant report

Variant	rs12041971
Chromosome Location	chr1:57645519-57645520
allele	C/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:26)

rs_ID	r²[population]
rs10489464	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11206988	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11206991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806749	1.00[CHB][hapmap]
rs12026905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12077019	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565136	1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes]
rs17115220	1.00[CHB][hapmap]
rs17115247	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476568	1.00[CHB][hapmap]
rs484064	1.00[CHB][hapmap]
rs490793	1.00[CHB][hapmap]
rs510824	1.00[CHB][hapmap]
rs513259	1.00[CHB][hapmap]
rs535415	1.00[CHB][hapmap]
rs537307	1.00[CHB][hapmap]
rs546020	1.00[CHB][hapmap]
rs550511	1.00[CHB][hapmap]
rs553453	1.00[CHB][hapmap]
rs564665	1.00[CHB][hapmap]
rs578962	1.00[CHB][hapmap]
rs579057	1.00[CHB][hapmap]
rs74074117	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074241	1.00[ASN][1000 genomes]
rs7542527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs9970799	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	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	chr1:57644800-57645600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:57644800-57645800	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr1:57644800-57646000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:57644800-57646800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr1:57645200-57645600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:57645400-57645800	Enhancers	HUES48 Cell Line	embryonic stem cell

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