Variant report

Variant	rs1223541
Chromosome Location	chr6:13159891-13159892
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1150607	0.93[CHD][hapmap];0.81[GIH][hapmap];0.82[MEX][hapmap]
rs1223531	0.88[JPT][hapmap]
rs1223534	0.88[JPT][hapmap]
rs1223538	0.85[CHD][hapmap];0.88[JPT][hapmap]
rs1223544	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1223545	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1223547	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1223548	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1223549	0.85[GIH][hapmap];0.81[MEX][hapmap]
rs1228529	0.94[CEU][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16873711	0.85[YRI][hapmap]
rs9463499	0.81[YRI][hapmap]
rs9463532	0.81[YRI][hapmap]
rs9473639	0.85[YRI][hapmap]

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

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13150000-13175600	Weak transcription	Lung	lung
2	chr6:13153400-13178000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:13153600-13164400	Weak transcription	Brain Germinal Matrix	brain
4	chr6:13153600-13167200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:13153600-13178200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:13153600-13178200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:13153800-13160800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:13153800-13168000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:13153800-13184200	Weak transcription	Aorta	Aorta
10	chr6:13154000-13175600	Weak transcription	Fetal Heart	heart
11	chr6:13157000-13164600	Weak transcription	Pancreas	Pancrea
12	chr6:13157000-13166000	Weak transcription	Brain Anterior Caudate	brain
13	chr6:13157400-13160600	Weak transcription	Left Ventricle	heart
14	chr6:13158200-13160000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:13158400-13160000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:13159200-13160000	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:13159200-13160000	Enhancers	HSMM	muscle
18	chr6:13159200-13160200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr6:13159200-13160600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr6:13159200-13181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:13159600-13160000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:13159600-13178400	Weak transcription	Right Ventricle	heart
23	chr6:13159800-13165800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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