Variant report

Variant	rs3742866
Chromosome Location	chr14:68008792-68008793
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68008274..68010027-chr14:68011299..68013623,2	K562	blood:
2	chr14:67993812..67995992-chr14:68006775..68009101,2	K562	blood:
3	chr14:67826062..67828511-chr14:68007056..68009921,3	MCF-7	breast:
4	chr14:67997232..68003099-chr14:68003235..68008915,12	K562	blood:
5	chr14:67999470..68001789-chr14:68008159..68009675,2	MCF-7	breast:
6	chr14:68005520..68007606-chr14:68008009..68010384,2	MCF-7	breast:
7	chr14:68007197..68009938-chr14:68013704..68015617,3	K562	blood:

Variant related genes	Relation type
ENSG00000198133	Chromatin interaction
ENSG00000134001	Chromatin interaction
ENSG00000100554	Chromatin interaction
ENSG00000054690	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10483797	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4899208	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58939454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59155762	0.86[ASN][1000 genomes]
rs60799856	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61266185	0.87[ASN][1000 genomes]
rs61988219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61988220	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61988242	0.90[ASN][1000 genomes]
rs61988243	0.95[ASN][1000 genomes]
rs61988244	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61988246	0.90[ASN][1000 genomes]
rs61988247	0.84[ASN][1000 genomes]
rs61988251	0.83[ASN][1000 genomes]
rs7150000	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3742866	APOBEC3C	trans	brain	seeQTL
rs3742866	C14orf181	cis	cerebellum	SCAN
rs3742866	ADAM20	cis	cerebellum	SCAN
rs3742866	PLEKHH1	cis	lymphoblastoid	seeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68000400-68044000	Weak transcription	Spleen	Spleen
2	chr14:68000800-68011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:68000800-68013000	Weak transcription	A549	lung
4	chr14:68001000-68010600	Weak transcription	Hela-S3	cervix
5	chr14:68001000-68024400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr14:68001400-68028400	Weak transcription	Brain Germinal Matrix	brain
7	chr14:68001600-68008800	Weak transcription	Fetal Brain Female	brain
8	chr14:68001800-68023600	Weak transcription	HepG2	liver
9	chr14:68002000-68065800	Weak transcription	Fetal Brain Male	brain
10	chr14:68003200-68008800	Weak transcription	Placenta	Placenta
11	chr14:68003200-68039800	Weak transcription	Fetal Kidney	kidney
12	chr14:68005400-68018200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr14:68005600-68010800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr14:68005600-68011000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr14:68005600-68023600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr14:68005800-68042400	Weak transcription	NHEK	skin
17	chr14:68006200-68011200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr14:68006400-68009800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr14:68006600-68010000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:68006800-68009400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr14:68006800-68009800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr14:68007800-68009000	Active TSS	Duodenum Mucosa	Duodenum
23	chr14:68008000-68009000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr14:68008000-68009000	Active TSS	Stomach Mucosa	stomach
25	chr14:68008000-68009200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr14:68008000-68009200	Active TSS	Rectal Smooth Muscle	rectum
27	chr14:68008200-68008800	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr14:68008200-68008800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
29	chr14:68008200-68009000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
30	chr14:68008200-68009000	Active TSS	Fetal Intestine Large	intestine
31	chr14:68008200-68009000	Active TSS	Fetal Intestine Small	intestine
32	chr14:68008200-68009000	Bivalent/Poised TSS	Fetal Stomach	stomach
33	chr14:68008200-68009200	Active TSS	H9 Cell Line	embryonic stem cell
34	chr14:68008200-68009200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr14:68008200-68009200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr14:68008200-68009200	Active TSS	Colonic Mucosa	Colon
37	chr14:68008200-68009200	Bivalent Enhancer	Fetal Thymus	thymus
38	chr14:68008200-68009200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
39	chr14:68008200-68009400	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr14:68008200-68011200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr14:68008400-68008800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr14:68008400-68008800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
43	chr14:68008400-68008800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
44	chr14:68008400-68008800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
45	chr14:68008400-68008800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr14:68008400-68008800	Active TSS	K562	blood
47	chr14:68008400-68009000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr14:68008400-68009000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr14:68008400-68009000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr14:68008400-68009000	Bivalent/Poised TSS	Primary T cells from cord blood	blood

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