Variant report

Variant	rs4902489
Chromosome Location	chr14:68041915-68041916
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:68000150..68001076-chr14:68041436..68042021,2	MCF-7	breast:
2	chr14:68040065..68042672-chr14:68048845..68051294,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054690	Chromatin interaction
ENSG00000198133	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11547225	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11625701	0.94[EUR][1000 genomes]
rs2236232	0.88[EUR][1000 genomes]
rs36113087	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902493	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902495	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902498	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7152499	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4902489	PIGH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68000400-68044000	Weak transcription	Spleen	Spleen
2	chr14:68002000-68065800	Weak transcription	Fetal Brain Male	brain
3	chr14:68005800-68042400	Weak transcription	NHEK	skin
4	chr14:68008800-68052200	Weak transcription	Left Ventricle	heart
5	chr14:68009000-68044800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:68009000-68050400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr14:68009200-68045200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr14:68011800-68045000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr14:68011800-68054600	Weak transcription	Hela-S3	cervix
10	chr14:68012000-68045000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr14:68013400-68052600	Weak transcription	Aorta	Aorta
12	chr14:68018600-68042400	Weak transcription	Right Ventricle	heart
13	chr14:68022800-68053000	Weak transcription	Lung	lung
14	chr14:68026400-68057400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr14:68026600-68054400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr14:68026600-68055200	Weak transcription	HMEC	breast
17	chr14:68027600-68045400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr14:68029800-68042600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr14:68030000-68042200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr14:68030000-68042600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr14:68030000-68044800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr14:68032600-68042200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr14:68034000-68043800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr14:68034400-68043000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr14:68034400-68052400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr14:68034600-68043000	Weak transcription	Esophagus	oesophagus
27	chr14:68034600-68057000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:68034800-68044800	Weak transcription	Adipose Nuclei	Adipose
29	chr14:68034800-68047200	Weak transcription	Stomach Mucosa	stomach
30	chr14:68036800-68052400	Weak transcription	Fetal Thymus	thymus
31	chr14:68038400-68042200	Weak transcription	Colonic Mucosa	Colon
32	chr14:68038400-68052200	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr14:68038400-68052400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:68038600-68042400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:68038600-68057800	Strong transcription	Brain Cingulate Gyrus	brain
36	chr14:68039200-68043000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr14:68039200-68046000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr14:68039400-68044000	Strong transcription	Placenta	Placenta
39	chr14:68039400-68049000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr14:68039400-68049200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr14:68039400-68049400	Strong transcription	Fetal Stomach	stomach
42	chr14:68039400-68057200	Strong transcription	Brain Germinal Matrix	brain
43	chr14:68039400-68057400	Strong transcription	Brain Anterior Caudate	brain
44	chr14:68039600-68044600	Strong transcription	Gastric	stomach
45	chr14:68039600-68046200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr14:68039600-68046800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr14:68039600-68049400	Strong transcription	Brain Angular Gyrus	brain
48	chr14:68039600-68061000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr14:68039800-68048600	Strong transcription	Fetal Brain Female	brain
50	chr14:68040000-68043200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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