Variant report

Variant	rs4512947
Chromosome Location	chr13:30466869-30466870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr13:30466820-30467172	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr13:30466241-30466906	H1-neurons	neurons:	n/a	n/a
3	REST	chr13:30465968-30467087	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
LINC00297	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11618268	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1590501	0.80[EUR][1000 genomes]
rs2388238	0.80[ASN][1000 genomes]
rs2388248	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs278040	0.88[EUR][1000 genomes]
rs6490432	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7987218	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7994929	0.80[EUR][1000 genomes]
rs9314986	0.82[EUR][1000 genomes]
rs9508585	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9579494	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998751	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3403452	chr13:30466852-30468000	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4512947	SLC7A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30452200-30468000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:30452200-30468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:30452600-30472200	Weak transcription	Ovary	ovary
4	chr13:30462000-30468200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:30462400-30468200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr13:30463000-30467600	Weak transcription	Fetal Lung	lung
7	chr13:30463000-30468000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:30463000-30476400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr13:30463400-30468000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr13:30463600-30468000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:30465200-30467000	Enhancers	Brain Substantia Nigra	brain
12	chr13:30466000-30467000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:30466000-30467000	Enhancers	Brain Anterior Caudate	brain
14	chr13:30466000-30467000	Enhancers	Brain Hippocampus Middle	brain
15	chr13:30466200-30467000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:30466200-30467000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr13:30466200-30467000	Enhancers	Brain Cingulate Gyrus	brain
18	chr13:30466200-30467000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr13:30466400-30467000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:30466400-30467000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:30466600-30467000	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr13:30466600-30467600	Weak transcription	NHDF-Ad	bronchial
23	chr13:30466600-30468000	Weak transcription	Esophagus	oesophagus
24	chr13:30466600-30468200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr13:30466800-30467800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr13:30466800-30468000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr13:30466800-30468000	Weak transcription	Pancreas	Pancrea
28	chr13:30466800-30468200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr13:30466800-30468400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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