Variant report

Variant	rs6554056
Chromosome Location	chr4:53721466-53721467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53713812..53716438-chr4:53719850..53722220,2	K562	blood:
2	chr4:53718830..53724031-chr4:53726765..53729736,6	MCF-7	breast:
3	chr4:53716501..53719430-chr4:53720319..53723628,3	K562	blood:
4	chr4:53577122..53581435-chr4:53720877..53725671,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128045	Chromatin interaction
ENSG00000226950	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000264585	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10003908	0.81[AMR][1000 genomes]
rs10016904	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10023440	0.83[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10026162	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10032190	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11940896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941841	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11947787	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4864676	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4864678	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4864680	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4864685	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62336790	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62338810	0.86[ASN][1000 genomes]
rs6838718	0.84[GIH][hapmap]
rs6844680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs730246	0.82[AMR][1000 genomes]
rs730247	0.82[AMR][1000 genomes]
rs731073	0.82[AMR][1000 genomes]
rs7663943	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7692692	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8287	0.89[ASW][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs881743	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs936690	0.90[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs962416	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9995861	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3431167	chr4:53721367-53721742	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53716000-53722200	Enhancers	Fetal Heart	heart
2	chr4:53716600-53721600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:53718000-53723600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr4:53719200-53721800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:53719200-53721800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:53719200-53723800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:53719800-53727400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:53719800-53727400	Weak transcription	Ovary	ovary
9	chr4:53720400-53722400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:53720600-53722200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr4:53720600-53722400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:53720600-53727800	Weak transcription	Aorta	Aorta
13	chr4:53720600-53728000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:53720800-53722400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:53721000-53721600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:53721000-53721800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:53721000-53722000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr4:53721000-53722200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr4:53721200-53721600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:53721400-53721600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:53721400-53721800	Enhancers	H1 Cell Line	embryonic stem cell
22	chr4:53721400-53721800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:53721400-53722000	Enhancers	Primary hematopoietic stem cells	blood
24	chr4:53721400-53722000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr4:53721400-53722200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:53721400-53722200	Enhancers	Fetal Brain Male	brain
27	chr4:53721400-53722400	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr4:53721400-53726000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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