Variant report

Variant	rs11630856
Chromosome Location	chr15:77858569-77858570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr15:77858541-77858764	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr15:77858488-77858835	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr15:77858417-77858941	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr15:77858468-77858866	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr15:77858483-77858784	H1-hESC	embryonic stem cell:	n/a	n/a

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:

Variant related genes	Relation type
ENSG00000259420	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1104815	0.89[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11630235	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11635834	0.96[ASN][1000 genomes]
rs12593629	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2003883	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2667757	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886517	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4886879	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886880	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7170855	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8039399	0.80[CEU][hapmap]
rs8040227	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868298	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs964990	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11630856	HMG20A	cis	parietal	SCAN
rs11630856	CYP1A2	cis	cerebellum	SCAN
rs11630856	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs11630856	LOXL1	cis	parietal	SCAN
rs11630856	STRA6	cis	cerebellum	SCAN
rs11630856	CHRNA5	cis	parietal	SCAN

Chromatin state (count:29 , 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	chr15:77855800-77858600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:77856400-77860400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:77857000-77859000	Enhancers	Brain Germinal Matrix	brain
7	chr15:77857200-77859000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr15:77857200-77862600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:77857400-77858800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr15:77857400-77859400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:77857400-77862000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:77857600-77859000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr15:77857600-77860600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:77857600-77860800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:77857800-77858600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr15:77857800-77859200	Weak transcription	Brain Anterior Caudate	brain
17	chr15:77857800-77859400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:77857800-77859600	Weak transcription	Brain Angular Gyrus	brain
19	chr15:77857800-77859800	Weak transcription	Fetal Brain Female	brain
20	chr15:77857800-77860200	Weak transcription	Brain Substantia Nigra	brain
21	chr15:77858000-77858600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr15:77858200-77859200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:77858200-77859200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:77858200-77859600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:77858200-77860000	Weak transcription	Fetal Lung	lung
26	chr15:77858200-77860800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:77858400-77858600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr15:77858400-77860200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:77858400-77860600	Weak transcription	Fetal Brain Male	brain

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