Variant report

Variant	rs6428408
Chromosome Location	chr1:197475085-197475086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197473401..197475790-chr1:197961530..197964182,2	K562	blood:
2	chr1:197473765..197476231-chr1:197480275..197482874,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB41-4	chr1:197475064-197476148	NONHSAT008627

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10158300	1.00[AMR][1000 genomes]
rs1024920	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs1028785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494753	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10494759	1.00[CHB][hapmap];1.00[AMR][1000 genomes]
rs10737689	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10737690	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10737691	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10754226	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs10801610	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10801611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10801615	1.00[AMR][1000 genomes]
rs10922241	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10922245	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12089070	1.00[JPT][hapmap]
rs1359458	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1362940	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1408841	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1421389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1421396	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1421398	1.00[AMR][1000 genomes]
rs1558975	1.00[AMR][1000 genomes]
rs1570809	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1582409	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16841893	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1862011	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs1886627	1.00[AMR][1000 genomes]
rs1923757	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1977330	1.00[AMR][1000 genomes]
rs2013617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2146484	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2147771	1.00[AMR][1000 genomes]
rs3790737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3902061	1.00[AMR][1000 genomes]
rs4244150	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4427436	1.00[AMR][1000 genomes]
rs4428919	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4477311	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4915243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs4915547	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4915548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6428407	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6428409	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6662893	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6676028	0.87[AFR][1000 genomes]
rs6678240	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6678776	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6685459	0.83[AFR][1000 genomes]
rs7515671	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7519686	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7543631	1.00[AMR][1000 genomes]
rs7553327	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs942050	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs981520	1.00[AMR][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	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521647	chr1:197464448-197529218	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv4010	chr1:197471463-197511397	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197467200-197499000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:197472200-197477800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:197473800-197479200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:197474000-197481600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:197475000-197484800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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