Variant report

Variant	rs1038248
Chromosome Location	chr8:9040858-9040859
allele	A/C
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	EP300	chr8:9039642-9041712	SK-N-SH	brain:	n/a	chr8:9040715-9040729
2	POLR2A	chr8:9040352-9040866	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr8:9040405-9040869	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9040629..9042906-chr8:9043135..9044982,2	K562	blood:

Variant related genes	Relation type
ENSG00000253252	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs106380	0.90[ASN][1000 genomes]
rs1994020	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367543	0.90[ASN][1000 genomes]
rs439989	0.88[ASN][1000 genomes]
rs6999694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7003070	1.00[ASN][1000 genomes]
rs7819833	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1022328	chr8:8954003-9061281	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv610206	chr8:8961017-9162048	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv949434	chr8:8993551-9318404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1016574	chr8:9007186-9061281	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv539461	chr8:9007186-9061281	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1018847	chr8:9017110-9216354	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1022967	chr8:9023771-9261351	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv539462	chr8:9023771-9261351	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv890339	chr8:9029413-9110822	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv890340	chr8:9029413-9121398	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv1025197	chr8:9037251-9116414	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1038248	CTSB	cis	cerebellum	SCAN
rs1038248	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs1038248	CLDN23	cis	multi-tissue	Pritchard
rs1038248	DEFB134	cis	parietal	SCAN
rs1038248	MFHAS1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9028400-9045200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:9035400-9042200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr8:9038200-9044200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:9038800-9041000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr8:9039400-9041000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr8:9039800-9042600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr8:9040000-9042400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr8:9040200-9041000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr8:9040200-9041000	Enhancers	Brain Substantia Nigra	brain
10	chr8:9040200-9041400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr8:9040200-9041400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr8:9040200-9041400	Enhancers	Brain Anterior Caudate	brain
13	chr8:9040200-9041600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr8:9040200-9042600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr8:9040200-9043400	Enhancers	Brain Cingulate Gyrus	brain
16	chr8:9040200-9043400	Enhancers	Brain Hippocampus Middle	brain
17	chr8:9040400-9041000	Enhancers	Brain Angular Gyrus	brain
18	chr8:9040400-9041400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr8:9040400-9041400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr8:9040400-9043400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr8:9040600-9041000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:9040600-9041000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr8:9040600-9043400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr8:9040600-9045000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr8:9040800-9041000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr8:9040800-9041200	Enhancers	H9 Cell Line	embryonic stem cell
27	chr8:9040800-9041600	Enhancers	K562	blood
28	chr8:9040800-9042600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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