Variant report

Variant	rs3214004
Chromosome Location	chr7:124720929-124720930
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	chr7:124720373..124721901-chr7:124740400..124743244,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1009450	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap]
rs10226033	0.83[CEU][hapmap]
rs10271646	0.81[CEU][hapmap]
rs10464674	0.85[ASN][1000 genomes]
rs10954065	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11532793	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11534064	0.83[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11536526	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12056290	0.80[ASN][1000 genomes]
rs1383748	0.87[ASN][1000 genomes]
rs1525613	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1568883	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17325193	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs17327014	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17327181	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs17327715	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17387389	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs17387591	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap]
rs2054586	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2170352	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2293346	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs36045816	0.81[AFR][1000 genomes]
rs4142718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55723877	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55859595	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55890146	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55905546	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56012154	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56056794	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56069273	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56216989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56269941	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56321835	0.81[AFR][1000 genomes]
rs650030	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs66478705	0.85[ASN][1000 genomes]
rs66756015	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66852389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669064	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs67146030	0.81[AFR][1000 genomes]
rs67277928	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67607629	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67680878	0.85[ASN][1000 genomes]
rs67817822	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67939974	0.81[AFR][1000 genomes]
rs68091803	0.81[AFR][1000 genomes]
rs685345	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6945199	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73225498	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73227531	0.84[ASN][1000 genomes]
rs9640831	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv889139	chr7:124600505-124767295	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv3394090	chr7:124602150-124900799	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv464708	chr7:124703756-124805279	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv608344	chr7:124703756-124805279	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv831119	chr7:124714009-124890119	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3214004	TMEM229A	cis	cerebellum	SCAN
rs3214004	LMOD2	cis	cerebellum	SCAN
rs3214004	IMPDH1	cis	parietal	SCAN
rs3214004	WASL	cis	cerebellum	SCAN

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

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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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