Variant report

Variant	rs6554150
Chromosome Location	chr4:54973200-54973201
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	chr4:54825736..54828574-chr4:54972078..54973978,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1132998	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1158401	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1158402	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2278141	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2278142	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3194383	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4293842	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4498189	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4565140	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7654979	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7655181	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7676331	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][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	nsv879018	chr4:54714753-55030375	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1003167	chr4:54732051-55081905	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv537096	chr4:54732051-55081905	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv594202	chr4:54943432-55011123	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv594203	chr4:54960005-55030375	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54969200-54973400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr4:54970600-54975200	Weak transcription	Pancreas	Pancrea
3	chr4:54970600-54975600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:54972200-54973200	Weak transcription	Brain Germinal Matrix	brain
5	chr4:54972200-54973200	Weak transcription	GM12878-XiMat	blood
6	chr4:54972200-54975200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:54972800-54975400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:54973000-54973200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
9	chr4:54973000-54973200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
10	chr4:54973000-54973200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
11	chr4:54973000-54973200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:54973000-54973600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr4:54973000-54973600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
14	chr4:54973000-54973600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
15	chr4:54973000-54973600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
16	chr4:54973000-54973600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
17	chr4:54973000-54975800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:54973000-54976000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:54973200-54973400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
20	chr4:54973200-54973400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
21	chr4:54973200-54973400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:54973200-54973800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr4:54973200-54974000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr4:54973200-54974200	Enhancers	Brain Germinal Matrix	brain
25	chr4:54973200-54974400	Enhancers	GM12878-XiMat	blood

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