Variant report

Variant	rs11941841
Chromosome Location	chr4:53725914-53725915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:53725892-53726023	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:53717769..53720549-chr4:53725622..53727129,2	K562	blood:
2	chr4:53723992..53727784-chr4:53728716..53731112,4	K562	blood:
3	chr4:53583825..53585724-chr4:53723633..53725976,2	K562	blood:

Variant related genes	Relation type
RASL11B	TF binding region
ENSG00000128045	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10003908	0.81[AMR][1000 genomes]
rs10016904	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10023440	0.83[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10026162	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10032190	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];0.99[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];0.87[ASN][1000 genomes]
rs2017237	0.81[CHD][hapmap];0.90[MKK][hapmap]
rs4864676	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4864678	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4864680	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4864685	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62336790	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62338810	0.85[ASN][1000 genomes]
rs6554056	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]
rs6838718	0.84[GIH][hapmap]
rs6844680	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]
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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7692692	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8287	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs881743	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936690	0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.84[AMR][1000 genomes]
rs962416	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9995861	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53719800-53727400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:53719800-53727400	Weak transcription	Ovary	ovary
3	chr4:53720600-53727800	Weak transcription	Aorta	Aorta
4	chr4:53720600-53728000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:53721400-53726000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:53722400-53727400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:53722400-53727600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:53723400-53727200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:53723600-53727600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:53725400-53726000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:53725400-53726000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:53725400-53726800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:53725400-53727200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr4:53725800-53726200	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr4:53725800-53727600	Enhancers	Fetal Brain Male	brain

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