Variant report

Variant	rs227401
Chromosome Location	chr14:70499880-70499881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:70498095..70500229-chr14:70502609..70504593,3	K562	blood:
2	chr14:70232945..70234905-chr14:70499269..70501298,2	MCF-7	breast:
3	chr14:70278462..70280862-chr14:70497209..70499902,2	MCF-7	breast:
4	chr14:70494747..70496910-chr14:70498282..70501125,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100650	Chromatin interaction

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

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

rs_ID	r²[population]
rs10130486	1.00[CHD][hapmap];0.89[JPT][hapmap]
rs1156444	1.00[ASN][1000 genomes]
rs1156445	1.00[ASN][1000 genomes]
rs13379247	1.00[GIH][hapmap]
rs17107580	0.85[CHD][hapmap]
rs17107663	1.00[ASN][1000 genomes]
rs1957449	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742914	1.00[CHB][hapmap];1.00[CHD][hapmap]

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	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv832824	chr14:70320639-70511401	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv817638	chr14:70489680-70500973	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs227401	GPHN	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70476000-70500000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr14:70486000-70500400	Weak transcription	Aorta	Aorta
3	chr14:70486400-70502800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr14:70494400-70500200	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr14:70494400-70500400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr14:70496800-70501000	Weak transcription	Pancreas	Pancrea
7	chr14:70497200-70503000	Weak transcription	Liver	Liver
8	chr14:70497400-70508400	Weak transcription	Fetal Brain Female	brain
9	chr14:70498200-70500200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr14:70498400-70500000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr14:70498400-70500000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr14:70498400-70500000	Enhancers	HMEC	breast
13	chr14:70498600-70500000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:70498600-70500000	Enhancers	Gastric	stomach
15	chr14:70498600-70500000	Enhancers	NHEK	skin
16	chr14:70498600-70500200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr14:70498600-70500400	Enhancers	HSMMtube	muscle
18	chr14:70498800-70500000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr14:70498800-70500000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr14:70498800-70500000	Enhancers	A549	lung
21	chr14:70498800-70500200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr14:70498800-70500200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr14:70498800-70500400	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr14:70498800-70500600	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr14:70499000-70500000	Enhancers	Placenta	Placenta
26	chr14:70499000-70500400	Enhancers	HepG2	liver
27	chr14:70499000-70500600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:70499000-70502400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr14:70499200-70500000	Enhancers	H1 Cell Line	embryonic stem cell
30	chr14:70499200-70500000	Enhancers	HSMM	muscle
31	chr14:70499200-70500200	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr14:70499200-70500600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr14:70499600-70500000	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr14:70499600-70500000	Enhancers	Spleen	Spleen
35	chr14:70499800-70500200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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