Variant report

Variant	rs389293
Chromosome Location	chr1:158228392-158228393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10797006	1.00[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10908644	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10908645	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11264949	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11264950	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11264952	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11486132	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11488686	0.83[EUR][1000 genomes]
rs12027881	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12038925	0.80[CEU][hapmap]
rs12077077	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12077284	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12089293	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12089433	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12095313	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12407446	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12409817	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12751238	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1813777	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1923141	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs366316	1.00[CEU][hapmap];0.92[GIH][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs378137	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs440710	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685958	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6687405	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs716221	0.80[CEU][hapmap]
rs7539343	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872480	chr1:158153526-158450238	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv508626	chr1:158161932-158242158	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1845799	chr1:158175976-158230829	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv831692	chr1:158223459-158392016	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv515666	chr1:158224825-158237062	Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs389293	GPATCH4	cis	parietal	SCAN
rs389293	S100A13	cis	parietal	SCAN
rs389293	S100A16	cis	cerebellum	SCAN
rs389293	AIM2	cis	cerebellum	SCAN
rs389293	RP11-404O13.4	cis	Thyroid	GTEx
rs389293	MRPL24	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158226000-158229400	Genic enhancers	Dnd41	blood
2	chr1:158227000-158229000	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr1:158227200-158229000	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:158227400-158228600	Enhancers	Primary T cells from cord blood	blood
5	chr1:158227400-158229200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:158227600-158228400	Active TSS	Fetal Thymus	thymus
7	chr1:158227600-158228800	Enhancers	Primary B cells from cord blood	blood
8	chr1:158227800-158228400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr1:158228000-158228400	Flanking Active TSS	Thymus	Thymus

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