Variant report

Variant	rs11940896
Chromosome Location	chr4:53720373-53720374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53717769..53720549-chr4:53725622..53727129,2	K562	blood:
2	chr4:53715750..53717744-chr4:53718273..53721166,2	MCF-7	breast:
3	chr4:53713812..53716438-chr4:53719850..53722220,2	K562	blood:
4	chr4:53718830..53724031-chr4:53726765..53729736,6	MCF-7	breast:
5	chr4:53716501..53719430-chr4:53720319..53723628,3	K562	blood:

Variant related genes	Relation type
ENSG00000128045	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

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];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10026162	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10032190	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11941841	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];0.88[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	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62336790	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62338810	0.86[ASN][1000 genomes]
rs6554056	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]
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];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];0.97[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];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs881743	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[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	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53709400-53721000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:53715200-53721000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr4:53716000-53722200	Enhancers	Fetal Heart	heart
4	chr4:53716600-53721600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:53717600-53720800	Enhancers	NHDF-Ad	bronchial
6	chr4:53718000-53720600	Enhancers	NHLF	lung
7	chr4:53718000-53723600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr4:53718600-53720600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr4:53718600-53720600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr4:53718600-53720600	Enhancers	HSMMtube	muscle
11	chr4:53718600-53720800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:53718800-53720400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:53719000-53720400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:53719000-53720400	Enhancers	HSMM	muscle
15	chr4:53719000-53720600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:53719000-53720600	Enhancers	NHEK	skin
17	chr4:53719000-53720800	Enhancers	HMEC	breast
18	chr4:53719000-53721400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:53719200-53720400	Weak transcription	Right Ventricle	heart
20	chr4:53719200-53720600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:53719200-53720600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:53719200-53720600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:53719200-53721000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:53719200-53721000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr4:53719200-53721200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr4:53719200-53721400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:53719200-53721800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:53719200-53721800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:53719200-53723800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:53719400-53720800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:53719400-53721400	Weak transcription	Fetal Brain Male	brain
32	chr4:53719600-53720400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:53719600-53720600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:53719800-53721400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:53719800-53721400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:53719800-53727400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:53719800-53727400	Weak transcription	Ovary	ovary
38	chr4:53720000-53720600	Enhancers	Aorta	Aorta
39	chr4:53720000-53721400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:53720200-53720800	Enhancers	Fetal Muscle Leg	muscle

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