Variant report

Variant	rs278040
Chromosome Location	chr13:30459712-30459713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1033930	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11616444	1.00[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs11618268	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1590501	0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2388248	0.82[JPT][hapmap]
rs4512947	0.88[EUR][1000 genomes]
rs6490432	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs7987218	0.86[EUR][1000 genomes]
rs7994929	0.91[EUR][1000 genomes]
rs9314986	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9508573	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs9508585	0.80[EUR][1000 genomes]
rs9579494	0.84[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs278040	SLC7A1	cis	cerebellum	SCAN
rs278040	SLC7A1	Cis_1M	lymphoblastoid	RTeQTL
rs278040	SHISA2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30452200-30461400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:30452200-30468000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:30452200-30468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:30452600-30472200	Weak transcription	Ovary	ovary
5	chr13:30456200-30462800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr13:30458200-30460000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:30458200-30460000	Enhancers	Brain Angular Gyrus	brain
8	chr13:30458200-30460400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr13:30458200-30460800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr13:30458200-30460800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr13:30458200-30461000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr13:30458200-30461000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr13:30458200-30463400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:30458600-30460400	Weak transcription	Osteobl	bone
15	chr13:30458600-30462400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr13:30459000-30462000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:30459400-30460000	Enhancers	Brain Hippocampus Middle	brain
18	chr13:30459400-30460000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr13:30459400-30460200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr13:30459400-30460400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr13:30459400-30461000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:30459400-30461200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr13:30459400-30462000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr13:30459400-30462400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr13:30459400-30462800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr13:30459400-30463600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:30459600-30459800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr13:30459600-30459800	Enhancers	Brain Anterior Caudate	brain
29	chr13:30459600-30460000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:30459600-30460600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:30459600-30460600	Enhancers	Brain Substantia Nigra	brain
32	chr13:30459600-30461800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr13:30459600-30463400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr13:30459600-30463600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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