Variant report

Variant	rs9314986
Chromosome Location	chr13:30458737-30458738
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1033930	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11616444	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11618268	0.83[ASN][1000 genomes]
rs11620360	1.00[CHB][hapmap]
rs1590501	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278040	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4512947	0.82[EUR][1000 genomes]
rs6490432	0.82[EUR][1000 genomes]
rs7994929	0.97[EUR][1000 genomes]
rs912396	1.00[CHB][hapmap]
rs9508573	1.00[CEU][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Biliary atresia	20460270	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9314986	SLC7A1	cis	cerebellum	SCAN
rs9314986	SHISA2	cis	cerebellum	SCAN
rs9314986	EXOSC6	trans	cerebellum	SCAN
rs9314986	PAN3	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30449600-30458800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:30452200-30461400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:30452200-30468000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:30452200-30468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:30452600-30472200	Weak transcription	Ovary	ovary
6	chr13:30456000-30459200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:30456200-30462800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr13:30456400-30459200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr13:30457200-30459000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:30458200-30458800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr13:30458200-30458800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr13:30458200-30458800	Enhancers	Brain Anterior Caudate	brain
13	chr13:30458200-30458800	Enhancers	Brain Substantia Nigra	brain
14	chr13:30458200-30459000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr13:30458200-30459000	Enhancers	Brain Cingulate Gyrus	brain
16	chr13:30458200-30459000	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr13:30458200-30459400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr13:30458200-30459600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr13:30458200-30460000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:30458200-30460000	Enhancers	Brain Angular Gyrus	brain
21	chr13:30458200-30460400	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr13:30458200-30460800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr13:30458200-30460800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:30458200-30461000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr13:30458200-30461000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr13:30458200-30463400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr13:30458400-30458800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr13:30458400-30458800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:30458400-30459200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr13:30458400-30459400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr13:30458600-30458800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr13:30458600-30458800	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr13:30458600-30459000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr13:30458600-30459000	Enhancers	NH-A	brain
35	chr13:30458600-30460400	Weak transcription	Osteobl	bone
36	chr13:30458600-30462400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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