Variant report

Variant	rs731681
Chromosome Location	chr14:68010224-68010225
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68009818..68011946-chr14:68016473..68018334,2	K562	blood:
2	chr14:68005520..68007606-chr14:68008009..68010384,2	MCF-7	breast:
3	chr14:67999033..68001548-chr14:68008899..68011774,3	K562	blood:

Variant related genes	Relation type
ENSG00000054690	Chromatin interaction
ENSG00000198133	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10873205	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12435433	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17184938	0.90[LWK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs2064929	0.84[MEX][hapmap]
rs4144498	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4902479	0.85[GIH][hapmap];0.84[MEX][hapmap]
rs4902482	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs6573780	0.84[MEX][hapmap]
rs7141506	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7147529	0.87[GIH][hapmap];0.84[MEX][hapmap]
rs731680	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs753682	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9671543	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9671816	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9671980	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs731681	PLEKHH1	cis	Thyroid	GTEx
rs731681	RAB15	cis	cerebellum	SCAN
rs731681	PLEKHH1	cis	cerebellum	SCAN

Chromatin state (count:63 , 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	chr14:68001800-68023600	Weak transcription	HepG2	liver
8	chr14:68002000-68065800	Weak transcription	Fetal Brain Male	brain
9	chr14:68003200-68039800	Weak transcription	Fetal Kidney	kidney
10	chr14:68005400-68018200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr14:68005600-68010800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:68005600-68011000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr14:68005600-68023600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr14:68005800-68042400	Weak transcription	NHEK	skin
15	chr14:68006200-68011200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr14:68008200-68011200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr14:68008600-68010400	Genic enhancers	Brain Anterior Caudate	brain
18	chr14:68008600-68010400	Genic enhancers	Brain Cingulate Gyrus	brain
19	chr14:68008600-68010800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr14:68008600-68011200	Genic enhancers	Brain Hippocampus Middle	brain
21	chr14:68008800-68011200	Strong transcription	Fetal Brain Female	brain
22	chr14:68008800-68012200	Strong transcription	Placenta	Placenta
23	chr14:68008800-68013400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr14:68008800-68013800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr14:68008800-68052200	Weak transcription	Left Ventricle	heart
26	chr14:68009000-68011600	Genic enhancers	Brain Substantia Nigra	brain
27	chr14:68009000-68013800	Weak transcription	Pancreas	Pancrea
28	chr14:68009000-68016400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr14:68009000-68022400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr14:68009000-68024800	Weak transcription	Gastric	stomach
31	chr14:68009000-68044800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr14:68009000-68050400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr14:68009200-68010600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr14:68009200-68011000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr14:68009200-68012200	Weak transcription	K562	blood
36	chr14:68009200-68014000	Weak transcription	Fetal Stomach	stomach
37	chr14:68009200-68016400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr14:68009200-68020200	Weak transcription	Stomach Mucosa	stomach
39	chr14:68009200-68023800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr14:68009200-68024000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr14:68009200-68024600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr14:68009200-68040400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr14:68009200-68045200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr14:68009400-68010400	Enhancers	Duodenum Mucosa	Duodenum
45	chr14:68009400-68010800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr14:68009400-68011000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr14:68009400-68012400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr14:68009600-68010800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr14:68009600-68011600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr14:68009600-68013600	Weak transcription	Colonic Mucosa	Colon

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