Variant report

Variant	rs10461354
Chromosome Location	chr4:55541165-55541166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10461353	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10488844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10488845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10488846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237024	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2855772	0.85[CEU][hapmap]
rs3796767	0.82[CHB][hapmap];0.97[EUR][1000 genomes]
rs3796768	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55958262	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57500613	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6834579	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6843170	0.85[CEU][hapmap]
rs73818375	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73818378	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73818380	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73818381	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS 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

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55534400-55542000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:55535000-55541800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:55535000-55544800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:55535600-55541600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:55536000-55541600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:55536200-55541800	Weak transcription	Fetal Brain Male	brain
7	chr4:55536200-55542000	Weak transcription	Lung	lung
8	chr4:55536400-55541400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:55536400-55541800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:55536400-55542000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:55536400-55542000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:55537000-55541400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:55537600-55554000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr4:55539200-55549800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:55539600-55545400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:55540200-55541800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:55540400-55543000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:55540400-55546200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:55540600-55541600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:55540800-55541200	Weak transcription	Fetal Brain Female	brain
21	chr4:55541000-55542400	Enhancers	Brain Germinal Matrix	brain
22	chr4:55541000-55543400	Enhancers	HUES48 Cell Line	embryonic stem cell

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