Variant report

Variant	rs6710329
Chromosome Location	chr2:178942302-178942303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:178940431..178942693-chr2:179060357..179062621,2	K562	blood:
2	chr2:178757808..178759787-chr2:178940377..178942583,2	K562	blood:
3	chr2:178939852..178942987-chr2:178976321..178978354,3	K562	blood:
4	chr2:178940677..178943272-chr2:178945277..178948244,4	K562	blood:
5	chr2:178940297..178942724-chr2:178946031..178947901,2	K562	blood:
6	chr2:178935372..178939354-chr2:178942023..178945915,4	K562	blood:
7	chr2:178932912..178934541-chr2:178939711..178942332,2	K562	blood:
8	chr2:178940999..178943053-chr2:178957174..178959156,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000155636	Chromatin interaction
ENSG00000128655	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10176475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10198111	0.88[CHB][hapmap]
rs10432485	0.94[JPT][hapmap]
rs11674668	0.83[CHB][hapmap]
rs11886139	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11887974	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11899905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13408924	0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1347441	0.88[CHB][hapmap]
rs1369515	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1369517	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1435571	0.84[ASW][hapmap];0.93[CEU][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap]
rs1852502	0.82[CHD][hapmap]
rs2034255	0.87[ASN][1000 genomes]
rs2043547	0.82[CHB][hapmap]
rs2163647	1.00[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap];0.90[ASN][1000 genomes]
rs2217838	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4300869	0.84[ASW][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs56103916	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6433709	0.88[CHB][hapmap]
rs6709256	0.83[CHB][hapmap]
rs6709343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs6714047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6738461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6740828	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6754705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7583491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7608073	0.82[CHB][hapmap]
rs9288014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	nsv533377	chr2:178718801-178963463	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv875451	chr2:178748294-178953409	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv583739	chr2:178942302-178993562	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6710329	AGPS	cis	lymphoblastoid	seeQTL
rs6710329	AGPS	cis	parietal	SCAN
rs6710329	TTN	cis	brain	BrainEAC
rs6710329	PLEKHA3	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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