Variant report

Variant	rs9671816
Chromosome Location	chr14:68002386-68002387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:67902911..67909562-chr14:67998675..68002742,8	MCF-7	breast:
2	chr14:67998150..68002925-chr14:68034555..68041423,8	MCF-7	breast:
3	chr14:67895676..67898158-chr14:68001898..68003463,2	MCF-7	breast:
4	chr14:67992735..67994453-chr14:68001902..68004897,2	MCF-7	breast:
5	chr14:67999015..68003161-chr14:68029425..68040471,13	MCF-7	breast:
6	chr14:67981602..67983778-chr14:68002059..68004467,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054690	Chromatin interaction
ENSG00000198133	Chromatin interaction
ENSG00000265993	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10873205	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12435433	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4144498	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7141506	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs731681	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs753682	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9671543	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9671980	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9671816	PLEKHH1	cis	Thyroid	GTEx
rs9671816	PPIAP6	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67999400-68002600	Active TSS	Brain Anterior Caudate	brain
2	chr14:67999400-68002600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr14:67999600-68002400	Active TSS	Brain Cingulate Gyrus	brain
4	chr14:67999600-68002400	Active TSS	Brain Hippocampus Middle	brain
5	chr14:68000400-68044000	Weak transcription	Spleen	Spleen
6	chr14:68000600-68002800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr14:68000600-68005200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:68000600-68007000	Weak transcription	Lung	lung
9	chr14:68000800-68004200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr14:68000800-68004800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr14:68000800-68005000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:68000800-68005000	Weak transcription	Adipose Nuclei	Adipose
13	chr14:68000800-68005000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr14:68000800-68005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr14:68000800-68011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr14:68000800-68013000	Weak transcription	A549	lung
17	chr14:68001000-68004400	Weak transcription	HMEC	breast
18	chr14:68001000-68004800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr14:68001000-68004800	Weak transcription	NHEK	skin
20	chr14:68001000-68005000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr14:68001000-68005200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr14:68001000-68005200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr14:68001000-68005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr14:68001000-68005400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr14:68001000-68005800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr14:68001000-68007600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr14:68001000-68008000	Weak transcription	K562	blood
28	chr14:68001000-68010600	Weak transcription	Hela-S3	cervix
29	chr14:68001000-68024400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr14:68001200-68002400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr14:68001200-68002800	Weak transcription	Fetal Kidney	kidney
32	chr14:68001200-68002800	Weak transcription	Placenta	Placenta
33	chr14:68001200-68004400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr14:68001200-68004600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr14:68001200-68005000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr14:68001200-68007400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr14:68001400-68005000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr14:68001400-68007600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr14:68001400-68028400	Weak transcription	Brain Germinal Matrix	brain
40	chr14:68001600-68003600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr14:68001600-68008800	Weak transcription	Fetal Brain Female	brain
42	chr14:68001800-68007000	Weak transcription	Fetal Intestine Large	intestine
43	chr14:68001800-68023600	Weak transcription	HepG2	liver
44	chr14:68002000-68002800	Active TSS	Brain Angular Gyrus	brain
45	chr14:68002000-68003400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr14:68002000-68006400	Weak transcription	Fetal Intestine Small	intestine
47	chr14:68002000-68065800	Weak transcription	Fetal Brain Male	brain
48	chr14:68002200-68002400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr14:68002200-68002600	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr14:68002200-68003200	Genic enhancers	Pancreas	Pancrea

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