Variant report

Variant	rs8038465
Chromosome Location	chr15:73978337-73978338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73923335..73928580-chr15:73974636..73980559,10	MCF-7	breast:
2	chr15:73923214..73925755-chr15:73977792..73979713,2	K562	blood:
3	chr15:73921937..73932817-chr15:73973872..73983627,19	MCF-7	breast:
4	chr15:73975048..73981150-chr15:73987719..73994346,13	MCF-7	breast:
5	chr15:73976691..73979215-chr15:74216849..74218653,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129038	Chromatin interaction
ENSG00000156642	Chromatin interaction
ENSG00000103855	Chromatin interaction
ENSG00000261801	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11072434	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs11574488	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11574495	0.88[CEU][hapmap]
rs11852484	0.88[EUR][1000 genomes]
rs12591553	0.81[CEU][hapmap]
rs12594627	0.92[CEU][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2291011	0.81[EUR][1000 genomes]
rs2291013	0.81[EUR][1000 genomes]
rs3816661	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs3935942	0.93[EUR][1000 genomes]
rs61012032	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs67257650	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs8032531	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs8032727	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs8041181	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs8041523	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037540	chr15:73712637-73982420	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3434440	chr15:73975149-73978997	Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Liver enzyme levels (gamma-glutamyl transferase)	22001757	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8038465	CD276	cis	multi-tissue	Pritchard
rs8038465	CPLX3	cis	cerebellum	SCAN
rs8038465	LMAN1L	cis	cerebellum	SCAN
rs8038465	C15orf34	cis	cerebellum	SCAN
rs8038465	PML	cis	parietal	SCAN
rs8038465	NR2E3	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73976000-73978400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:73976000-73978600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:73976400-73978400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:73976400-73978400	Active TSS	Left Ventricle	heart
5	chr15:73977000-73978400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
6	chr15:73977000-73979000	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr15:73977200-73978400	Flanking Active TSS	HUVEC	blood vessel
8	chr15:73977200-73978600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr15:73977200-73979000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr15:73977400-73978800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:73977600-73978400	Weak transcription	Esophagus	oesophagus
12	chr15:73977600-73978400	Flanking Active TSS	Fetal Lung	lung
13	chr15:73977600-73978800	Flanking Active TSS	Fetal Brain Male	brain
14	chr15:73977600-73978800	Enhancers	Stomach Mucosa	stomach
15	chr15:73977600-73979600	Flanking Active TSS	Hela-S3	cervix
16	chr15:73977800-73978400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:73977800-73978400	Active TSS	Colonic Mucosa	Colon
18	chr15:73977800-73978400	Flanking Active TSS	Fetal Heart	heart
19	chr15:73977800-73978600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr15:73977800-73978600	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr15:73977800-73978600	Flanking Active TSS	Fetal Kidney	kidney
22	chr15:73977800-73978800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr15:73977800-73978800	Enhancers	Duodenum Mucosa	Duodenum
24	chr15:73977800-73979000	Enhancers	Brain Substantia Nigra	brain
25	chr15:73977800-73979000	Flanking Active TSS	HepG2	liver
26	chr15:73977800-73979600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:73977800-73979600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr15:73977800-73979800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:73977800-73979800	Enhancers	Pancreas	Pancrea
30	chr15:73977800-73981800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:73977800-73982400	Enhancers	Lung	lung
32	chr15:73978000-73978400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
33	chr15:73978000-73978400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:73978000-73978400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr15:73978000-73978400	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr15:73978000-73978400	Flanking Active TSS	Right Ventricle	heart
37	chr15:73978000-73978600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:73978000-73978600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr15:73978000-73978600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr15:73978000-73978600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr15:73978000-73978600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:73978000-73978600	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr15:73978000-73978600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr15:73978000-73978600	Flanking Active TSS	Placenta	Placenta
45	chr15:73978000-73978600	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr15:73978000-73978600	Weak transcription	A549	lung
47	chr15:73978000-73978800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr15:73978000-73978800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:73978000-73978800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr15:73978000-73979000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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