Variant report

Variant	rs11925380
Chromosome Location	chr3:61066520-61066521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11918956	1.00[EUR][1000 genomes]
rs11925426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17064433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2118812	1.00[EUR][1000 genomes]
rs41495354	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs56260470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56366514	1.00[EUR][1000 genomes]
rs56379111	1.00[EUR][1000 genomes]
rs58847767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59971851	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6763300	1.00[GIH][hapmap]
rs6774890	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73839213	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73839214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73839215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73839217	1.00[EUR][1000 genomes]
rs7609788	1.00[EUR][1000 genomes]
rs7610331	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7642143	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7644525	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs7644694	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7646887	1.00[CEU][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9820046	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876864	chr3:60952040-61103609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv915904	chr3:60952040-61125194	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1012510	chr3:60952040-61131709	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv536578	chr3:60952040-61131709	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv948633	chr3:60993915-61171279	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv834710	chr3:60995631-61148157	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2757873	chr3:61019003-61185558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv2756993	chr3:61064432-61119923	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61033600-61066600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:61063000-61067400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr3:61063800-61067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:61064200-61066600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:61064400-61066600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:61065200-61067600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:61065200-61067800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:61065800-61066600	Enhancers	Fetal Kidney	kidney
9	chr3:61065800-61067200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:61065800-61067400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:61065800-61067600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:61066000-61067200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:61066000-61067400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:61066200-61066600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:61066200-61067000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:61066400-61066600	Enhancers	Brain Anterior Caudate	brain
17	chr3:61066400-61066800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:61066400-61066800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:61066400-61066800	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr3:61066400-61067000	Enhancers	Brain Hippocampus Middle	brain
21	chr3:61066400-61067200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr3:61066400-61067400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:61066400-61067600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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