Variant report

Variant	rs512299
Chromosome Location	chr6:49704834-49704835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:49692689..49696652-chr6:49702639..49705030,4	K562	blood:
2	chr6:49703035..49705028-chr6:49750310..49752652,2	K562	blood:
3	chr6:49601909..49605014-chr6:49702815..49705548,4	K562	blood:
4	chr6:49702867..49705670-chr6:49708878..49713468,7	K562	blood:
5	chr6:49703675..49708245-chr6:49709607..49712140,5	K562	blood:
6	chr6:49602202..49605447-chr6:49703297..49710547,8	K562	blood:

Variant related genes	Relation type
ENSG00000112077	Chromatin interaction
ENSG00000096006	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1621948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168623	0.92[ASN][1000 genomes]
rs183115	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs184857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068681	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2104029	1.00[CHB][hapmap]
rs360541	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360542	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360543	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs360544	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360545	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360546	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360547	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs360548	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360555	0.95[ASN][1000 genomes]
rs3799688	0.88[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.86[MEX][hapmap]
rs483914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488132	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500032	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs502256	0.83[ASN][1000 genomes]
rs513343	1.00[JPT][hapmap]
rs521489	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521492	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553584	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555103	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56085173	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56148648	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs571257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584747	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs597544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614217	0.98[ASN][1000 genomes]
rs623996	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs626221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633319	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs643775	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458712	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs659190	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66909600	0.83[AMR][1000 genomes]
rs670624	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6922618	1.00[CHB][hapmap]
rs6925452	0.92[CHB][hapmap]
rs693929	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs696717	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699972	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs699974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs699982	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs699990	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs699991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs699993	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs699994	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs699996	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7760595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs780445	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs812969	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs512299	TRAM2	cis	parietal	SCAN
rs512299	IL17F	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49694200-49705400	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:49704600-49705600	Enhancers	K562	blood

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