Variant report

Variant	rs2388238
Chromosome Location	chr13:30468383-30468384
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UBL3-5	chr13:30468191-30468397	l_803_chr13:30467192-30468397_testes

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2388248	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4512947	0.80[ASN][1000 genomes]
rs6490432	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs6490433	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8000203	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8000402	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9508585	1.00[ASN][1000 genomes]
rs998751	0.84[EUR][1000 genomes];0.95[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2388238	SLC7A1	cis	cerebellum	SCAN
rs2388238	SLC7A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30452600-30472200	Weak transcription	Ovary	ovary
2	chr13:30463000-30476400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr13:30466800-30468400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr13:30467400-30468400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr13:30467600-30468600	Enhancers	NHDF-Ad	bronchial
6	chr13:30467800-30468400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:30467800-30468600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr13:30468000-30468600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr13:30468000-30468600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:30468000-30468600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr13:30468000-30468600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:30468000-30468600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr13:30468000-30468600	Enhancers	Esophagus	oesophagus
14	chr13:30468000-30468600	Enhancers	Gastric	stomach
15	chr13:30468000-30468600	Enhancers	Pancreas	Pancrea
16	chr13:30468000-30468600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr13:30468000-30468600	Enhancers	Stomach Mucosa	stomach
18	chr13:30468000-30468800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:30468000-30473800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr13:30468200-30468400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr13:30468200-30468400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr13:30468200-30468400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr13:30468200-30468600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:30468200-30468600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:30468200-30468600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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