Variant report

Variant	rs1223538
Chromosome Location	chr6:13158099-13158100
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13156962..13159022-chr6:13161516..13164006,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1223510	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1223520	1.00[CEU][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1223521	1.00[CEU][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1223527	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1223529	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1223531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1223534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1223541	0.85[CHD][hapmap];0.88[JPT][hapmap]
rs1223545	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs1223547	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs1937768	1.00[YRI][hapmap]
rs2186159	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35596191	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458677	0.92[EUR][1000 genomes]
rs6909002	0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600992	chr6:12961922-13218549	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1223538	ERVFRDE1	cis	cerebellum	SCAN
rs1223538	JARID2	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13142400-13159400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr6:13146000-13158400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:13146000-13159200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:13150000-13175600	Weak transcription	Lung	lung
5	chr6:13153400-13178000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:13153600-13159200	Weak transcription	Right Ventricle	heart
7	chr6:13153600-13164400	Weak transcription	Brain Germinal Matrix	brain
8	chr6:13153600-13167200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:13153600-13178200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:13153600-13178200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:13153800-13160800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:13153800-13168000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:13153800-13184200	Weak transcription	Aorta	Aorta
14	chr6:13154000-13175600	Weak transcription	Fetal Heart	heart
15	chr6:13156600-13159200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:13157000-13164600	Weak transcription	Pancreas	Pancrea
17	chr6:13157000-13166000	Weak transcription	Brain Anterior Caudate	brain
18	chr6:13157200-13159200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:13157400-13160600	Weak transcription	Left Ventricle	heart
20	chr6:13157600-13158200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:13157800-13158200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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