Variant report

Variant	rs12117865
Chromosome Location	chr1:77048617-77048618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12239615	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1369805	1.00[CHB][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17099155	0.92[MEX][hapmap]
rs17631994	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2574775	0.93[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2647392	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs315029	1.00[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs315030	0.94[EUR][1000 genomes]
rs315031	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs315060	1.00[CHB][hapmap]
rs315061	1.00[CHB][hapmap]
rs315078	1.00[CHB][hapmap]
rs315079	1.00[CHB][hapmap]
rs315081	1.00[CHB][hapmap]
rs341029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs369258	1.00[CEU][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs402112	1.00[CHB][hapmap]
rs425149	1.00[CHB][hapmap]
rs4300268	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4307606	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4336900	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4598537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61771660	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6593544	1.00[CHB][hapmap]
rs7541103	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7544201	0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997827	chr1:76929028-77201457	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428774	chr1:76971045-77075766	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv526433	chr1:77030764-77268215	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv508315	chr1:77040085-77134730	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12117865	ZZZ3	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77044000-77051800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:77045800-77049800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr1:77045800-77050600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr1:77047800-77050600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:77048000-77049200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr1:77048000-77049600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr1:77048000-77050200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:77048000-77050200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr1:77048200-77049200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:77048200-77050200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:77048400-77049600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:77048400-77049800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr1:77048600-77049400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:77048600-77049800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:77048600-77050200	Enhancers	HUES6 Cell Line	embryonic stem cell

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