Variant report

Variant	rs415838
Chromosome Location	chr2:77612535-77612536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10520185	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11126606	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs11676547	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs11693018	0.96[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap]
rs13025831	1.00[CEU][hapmap]
rs290016	0.89[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs290017	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs290018	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs290020	0.81[EUR][1000 genomes]
rs290024	0.85[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs290025	0.81[EUR][1000 genomes]
rs290027	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs290028	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs290029	0.81[EUR][1000 genomes]
rs290030	0.81[EUR][1000 genomes]
rs290032	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];0.97[ASN][1000 genomes]
rs290033	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs290034	0.92[CEU][hapmap]
rs378029	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs393564	0.81[CEU][hapmap]
rs407079	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs420117	0.81[AMR][1000 genomes]
rs427294	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs433156	0.92[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs435044	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs438859	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs619530	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs694136	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][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	nsv949670	chr2:77125218-77712607	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv874333	chr2:77315349-77798886	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv518504	chr2:77326832-78172786	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1004938	chr2:77347740-78186543	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv535783	chr2:77347740-78186543	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv529904	chr2:77347741-78186542	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv997329	chr2:77354560-78176285	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv834267	chr2:77534499-77708336	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv470473	chr2:77564243-77633888	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1004097	chr2:77575188-77706008	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv535784	chr2:77575188-77706008	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:77611000-77614000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:77611600-77614200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:77612000-77612800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:77612000-77612800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:77612200-77612800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr2:77612400-77612800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr2:77612400-77613400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:77612400-77614400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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