Variant report

Variant	rs753683
Chromosome Location	chr14:68005147-68005148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68003774..68006683-chr14:68064247..68065848,2	MCF-7	breast:
2	chr14:68004052..68005607-chr14:68020967..68023715,2	MCF-7	breast:
3	chr14:67997632..68001958-chr14:68003230..68007409,7	K562	blood:
4	chr14:67997232..68003099-chr14:68003235..68008915,12	K562	blood:
5	chr14:68004825..68008195-chr14:68010390..68013765,5	MCF-7	breast:
6	chr14:67997795..68000777-chr14:68005139..68007037,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054690	Chromatin interaction
ENSG00000198133	Chromatin interaction

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

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

rs_ID	r²[population]
rs11158681	0.87[CEU][hapmap]
rs11158682	0.87[CEU][hapmap]
rs11158684	0.87[CEU][hapmap]
rs17782224	0.95[CEU][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs2064929	0.80[CEU][hapmap]
rs2319842	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902479	0.87[CEU][hapmap]
rs4902482	0.80[CEU][hapmap]
rs4902483	0.87[CEU][hapmap]
rs4902487	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6573780	0.80[CEU][hapmap]
rs67138363	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7147529	0.84[CEU][hapmap]
rs7155887	0.92[EUR][1000 genomes]
rs9972155	0.91[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.88[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
rs753683	PLEKHH1	cis	cerebellum	SCAN
rs753683	FUT8	cis	parietal	SCAN
rs753683	ADAM20	cis	cerebellum	SCAN
rs753683	C14orf181	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68000400-68044000	Weak transcription	Spleen	Spleen
2	chr14:68000600-68005200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:68000600-68007000	Weak transcription	Lung	lung
4	chr14:68000800-68005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:68000800-68011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr14:68000800-68013000	Weak transcription	A549	lung
7	chr14:68001000-68005200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr14:68001000-68005200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr14:68001000-68005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr14:68001000-68005400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr14:68001000-68005800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr14:68001000-68007600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr14:68001000-68008000	Weak transcription	K562	blood
14	chr14:68001000-68010600	Weak transcription	Hela-S3	cervix
15	chr14:68001000-68024400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr14:68001200-68007400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr14:68001400-68007600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr14:68001400-68028400	Weak transcription	Brain Germinal Matrix	brain
19	chr14:68001600-68008800	Weak transcription	Fetal Brain Female	brain
20	chr14:68001800-68007000	Weak transcription	Fetal Intestine Large	intestine
21	chr14:68001800-68023600	Weak transcription	HepG2	liver
22	chr14:68002000-68006400	Weak transcription	Fetal Intestine Small	intestine
23	chr14:68002000-68065800	Weak transcription	Fetal Brain Male	brain
24	chr14:68003200-68008200	Weak transcription	Pancreas	Pancrea
25	chr14:68003200-68008400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr14:68003200-68008800	Weak transcription	Placenta	Placenta
27	chr14:68003200-68039800	Weak transcription	Fetal Kidney	kidney
28	chr14:68003400-68005400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr14:68004000-68006400	Enhancers	Brain Anterior Caudate	brain
30	chr14:68004000-68008200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:68004400-68005200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr14:68004400-68005400	Enhancers	Primary B cells from peripheral blood	blood
33	chr14:68004400-68005800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr14:68004400-68005800	Enhancers	HMEC	breast
35	chr14:68004400-68006200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr14:68004600-68005400	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr14:68004600-68005400	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr14:68004600-68005600	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr14:68004600-68005600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr14:68004800-68005400	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr14:68004800-68005800	Enhancers	NHEK	skin
42	chr14:68004800-68006000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr14:68004800-68006400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:68005000-68005200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr14:68005000-68005400	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr14:68005000-68005400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr14:68005000-68005600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr14:68005000-68005600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr14:68005000-68005600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr14:68005000-68005600	Enhancers	Skeletal Muscle Female	skeletal muscle

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