Variant report

Variant	rs17769870
Chromosome Location	chr16:77336479-77336480
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1025317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10459866	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1060547	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12051418	0.86[CEU][hapmap]
rs12149530	0.82[AMR][1000 genomes]
rs12149784	0.80[AMR][1000 genomes]
rs12599131	0.86[CEU][hapmap]
rs12918088	0.83[AMR][1000 genomes]
rs12923460	0.91[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12925274	0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12927388	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12930139	0.82[AMR][1000 genomes]
rs12931837	0.82[AMR][1000 genomes]
rs12933721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12934894	0.88[JPT][hapmap]
rs12935229	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12935394	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16945428	0.93[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17687224	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs17701840	0.82[AMR][1000 genomes]
rs17701900	0.82[AMR][1000 genomes]
rs17712814	0.82[AMR][1000 genomes]
rs17712821	0.82[AMR][1000 genomes]
rs17712844	0.82[AMR][1000 genomes]
rs17712926	0.93[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17712956	0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17712992	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17713035	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17713119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17713725	0.85[CEU][hapmap]
rs17769663	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17769712	0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17769748	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17769754	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17769760	0.83[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17769766	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17769937	0.86[CEU][hapmap]
rs2062578	0.86[CEU][hapmap]
rs34031278	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34371402	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34504566	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34617072	0.80[AMR][1000 genomes]
rs34807040	0.82[AMR][1000 genomes]
rs35076488	0.82[AMR][1000 genomes]
rs35292425	0.82[AMR][1000 genomes]
rs35296483	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35457602	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35559419	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35924034	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36045444	0.82[AMR][1000 genomes]
rs36076586	0.82[AMR][1000 genomes]
rs58027728	0.80[AMR][1000 genomes]
rs60755592	0.82[AMR][1000 genomes]
rs66515609	0.80[AMR][1000 genomes]
rs66771322	0.80[AMR][1000 genomes]
rs67261439	0.82[AMR][1000 genomes]
rs67426384	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67533522	0.80[AMR][1000 genomes]
rs71396107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72801605	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs934125	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9937032	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv1066258	chr16:77229953-77521919	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv542968	chr16:77229953-77521919	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2761916	chr16:77277005-77555833	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1059194	chr16:77281068-77745928	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv542969	chr16:77281068-77745928	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv934211	chr16:77281069-77396084	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1065714	chr16:77285659-77385518	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17769870	FA2H	cis	cerebellum	SCAN
rs17769870	ADAMTS18	cis	parietal	SCAN
rs17769870	ADAMTS18	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77311600-77344200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr16:77312000-77336600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr16:77328000-77357600	Weak transcription	Adipose Nuclei	Adipose
4	chr16:77329200-77389800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr16:77333200-77342000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr16:77333800-77338200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:77333800-77339600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:77334400-77339600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr16:77334400-77341600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr16:77334600-77341600	Weak transcription	NH-A	brain
11	chr16:77335800-77337000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:77335800-77341200	Weak transcription	HUVEC	blood vessel
13	chr16:77336000-77337200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr16:77336000-77337400	Enhancers	Primary T cells from cord blood	blood
15	chr16:77336200-77337200	Enhancers	Fetal Stomach	stomach
16	chr16:77336200-77337400	Enhancers	Brain Substantia Nigra	brain
17	chr16:77336200-77337600	Enhancers	Dnd41	blood
18	chr16:77336200-77338400	Weak transcription	A549	lung
19	chr16:77336400-77341800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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