Variant report

Variant	rs6730679
Chromosome Location	chr2:134282346-134282347
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	chr2:134279989..134282547-chr2:134284755..134287346,3	K562	blood:

Variant related genes	Relation type
ENSG00000176771	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10165238	0.82[CEU][hapmap]
rs1017366	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs10206425	1.00[CEU][hapmap]
rs11891880	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903204	0.81[EUR][1000 genomes]
rs13399787	1.00[CEU][hapmap]
rs13408209	1.00[CEU][hapmap]
rs16825505	1.00[CEU][hapmap]
rs16825509	1.00[CEU][hapmap]
rs16826050	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16826052	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16826544	1.00[JPT][hapmap]
rs17815418	1.00[CEU][hapmap]
rs60316439	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61578634	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720995	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732077	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72990470	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990471	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990476	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72990483	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72990486	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72990490	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72990493	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72990494	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72992306	0.81[EUR][1000 genomes]
rs72992325	0.81[EUR][1000 genomes]
rs72992334	0.81[EUR][1000 genomes]
rs72992339	0.81[EUR][1000 genomes]
rs72992347	0.81[EUR][1000 genomes]
rs72992351	0.81[EUR][1000 genomes]
rs72992377	0.81[EUR][1000 genomes]
rs73003136	1.00[EUR][1000 genomes]
rs73003138	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73003141	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73003144	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73003146	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73003147	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7340446	0.82[CEU][hapmap];1.00[EUR][1000 genomes]
rs7340510	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917399	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2830192	chr2:134259612-134311713	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6730679	PRELP	trans	brain	seeQTL
rs6730679	HP	trans	brain	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134268200-134290000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:134280800-134282400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:134281200-134282600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:134281400-134282400	Weak transcription	Ovary	ovary
5	chr2:134281600-134284200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:134282000-134285400	Enhancers	Fetal Lung	lung
7	chr2:134282200-134284600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:134282200-134286200	Enhancers	Fetal Brain Male	brain

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