Variant report

Variant	rs11149981
Chromosome Location	chr16:77370138-77370139
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10514411	0.86[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap]
rs10514412	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes]
rs12051144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12051395	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12051418	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12596175	1.00[AFR][1000 genomes]
rs12596195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12596198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12597784	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12597837	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12598787	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12599022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12599131	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12600056	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12600228	0.82[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1318020	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17687224	0.86[CEU][hapmap]
rs17713725	0.88[CHB][hapmap];0.87[EUR][1000 genomes]
rs17769937	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2062578	0.93[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes]
rs2650891	0.84[CHB][hapmap]
rs6564434	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs67076559	1.00[AFR][1000 genomes]
rs7192938	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs72487959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs866925	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs929890	1.00[AFR][1000 genomes]
rs9746317	0.86[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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
15	nsv457541	chr16:77353973-77389002	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv573124	chr16:77353973-77389002	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv3438223	chr16:77366876-77370224	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11149981	FA2H	cis	cerebellum	SCAN
rs11149981	ADAMTS18	cis	cerebellum	SCAN
rs11149981	ADAMTS18	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77329200-77389800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr16:77359400-77392800	Weak transcription	HUVEC	blood vessel
3	chr16:77365000-77383600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr16:77367400-77370600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:77369200-77371200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr16:77369200-77371400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr16:77369200-77371600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr16:77369400-77370600	Enhancers	Fetal Kidney	kidney
9	chr16:77369600-77370200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr16:77369600-77370200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr16:77369600-77370400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr16:77369600-77371400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr16:77369600-77371400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr16:77369600-77371400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr16:77369600-77371400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr16:77369600-77371600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr16:77369600-77371600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr16:77369800-77370400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr16:77369800-77370800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr16:77369800-77371000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr16:77369800-77371400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr16:77369800-77371400	Enhancers	H9 Cell Line	embryonic stem cell
23	chr16:77369800-77371400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr16:77369800-77371600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr16:77370000-77370200	Enhancers	Brain Angular Gyrus	brain
26	chr16:77370000-77370200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr16:77370000-77370400	Weak transcription	Brain Substantia Nigra	brain
28	chr16:77370000-77370800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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