Variant report

Variant	rs2682927
Chromosome Location	chr15:77859168-77859169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77856989..77859495-chr15:77861940..77865382,3	K562	blood:
2	chr15:77848566..77850112-chr15:77856631..77859198,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1055691	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635226	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11635634	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636231	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12902072	0.81[EUR][1000 genomes]
rs12902898	0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs12902948	0.81[EUR][1000 genomes]
rs12904200	0.81[EUR][1000 genomes]
rs12904208	0.81[EUR][1000 genomes]
rs12904533	0.81[EUR][1000 genomes]
rs12905044	0.81[EUR][1000 genomes]
rs12905318	0.81[EUR][1000 genomes]
rs12913005	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12914932	0.81[CEU][hapmap]
rs12917044	0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs12917431	0.81[EUR][1000 genomes]
rs2667775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682924	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55883527	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs907383	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs939488	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv904417	chr15:77851535-77935992	Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2682927	STRA6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77850600-77859600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr15:77855600-77859400	Enhancers	Brain Hippocampus Middle	brain
3	chr15:77855600-77862600	Enhancers	Brain Cingulate Gyrus	brain
4	chr15:77856400-77860400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:77857200-77862600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:77857400-77859400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:77857400-77862000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:77857600-77860600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:77857600-77860800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:77857800-77859200	Weak transcription	Brain Anterior Caudate	brain
11	chr15:77857800-77859400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:77857800-77859600	Weak transcription	Brain Angular Gyrus	brain
13	chr15:77857800-77859800	Weak transcription	Fetal Brain Female	brain
14	chr15:77857800-77860200	Weak transcription	Brain Substantia Nigra	brain
15	chr15:77858200-77859200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:77858200-77859200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:77858200-77859600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:77858200-77860000	Weak transcription	Fetal Lung	lung
19	chr15:77858200-77860800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:77858400-77860200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:77858400-77860600	Weak transcription	Fetal Brain Male	brain
22	chr15:77858600-77860400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:77858800-77861000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr15:77858800-77861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr15:77859000-77860800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:77859000-77860800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:77859000-77860800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:77859000-77862400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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