Variant report

Variant	rs8038920
Chromosome Location	chr15:78974545-78974546
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	chr15:78912983..78915101-chr15:78972644..78975199,2	K562	blood:
2	chr15:78970161..78972429-chr15:78973595..78976262,2	K562	blood:

Variant related genes	Relation type
ENSG00000080644	Chromatin interaction

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

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

rs_ID	r²[population]
rs11072787	0.83[YRI][hapmap]
rs12901241	0.82[EUR][1000 genomes]
rs12905641	0.90[EUR][1000 genomes]
rs12910237	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs28444683	0.84[EUR][1000 genomes]
rs34275594	0.91[EUR][1000 genomes]
rs34694149	0.90[EUR][1000 genomes]
rs35704045	0.81[EUR][1000 genomes]
rs58946838	0.87[EUR][1000 genomes]
rs61630816	0.90[EUR][1000 genomes]
rs7169223	0.83[EUR][1000 genomes]
rs7178007	0.90[EUR][1000 genomes]
rs7181405	0.92[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs922691	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv974713	chr15:78945824-78996783	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv457209	chr15:78949127-78986805	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv471256	chr15:78949127-78986805	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv570203	chr15:78949127-78986805	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	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
rs8038920	FAH	cis	parietal	SCAN
rs8038920	UBL7	cis	parietal	SCAN
rs8038920	CHRNA5	cis	cerebellum	SCAN
rs8038920	CHRNA5	cis	parietal	SCAN
rs8038920	IREB2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78966200-78977000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr15:78969400-78978000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:78971400-78975200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr15:78971800-78974600	Weak transcription	Spleen	Spleen
5	chr15:78971800-78975200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:78972000-78975200	Enhancers	Fetal Brain Male	brain
7	chr15:78972000-78977400	Weak transcription	HMEC	breast
8	chr15:78972000-78980000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:78972400-78975200	Enhancers	Primary hematopoietic stem cells	blood
10	chr15:78972400-78975200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr15:78972600-78975400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:78972800-78975200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr15:78972800-78975400	Enhancers	Fetal Brain Female	brain
14	chr15:78972800-78975400	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr15:78972800-78975800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr15:78973000-78974800	Enhancers	H9 Cell Line	embryonic stem cell
17	chr15:78973000-78974800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:78973200-78974800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr15:78973200-78975000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr15:78973200-78975400	Enhancers	Fetal Stomach	stomach
21	chr15:78973600-78974600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr15:78973600-78974800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr15:78973600-78974800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr15:78973600-78975000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr15:78973800-78974600	Bivalent Enhancer	Fetal Muscle Leg	muscle
26	chr15:78973800-78975000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr15:78974000-78977600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:78974200-78974600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:78974200-78976800	Weak transcription	Fetal Kidney	kidney
30	chr15:78974200-78977600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr15:78974200-78977600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:78974400-78975000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr15:78974400-78975400	Enhancers	Esophagus	oesophagus
34	chr15:78974400-78976800	Weak transcription	Fetal Thymus	thymus

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