Variant report

Variant	rs1439879
Chromosome Location	chr2:188943551-188943552
allele	A/G
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:34)

rs_ID	r²[population]
rs11674812	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11680607	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11680615	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11685836	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12466815	1.00[ASN][1000 genomes]
rs13002178	1.00[ASN][1000 genomes]
rs13035162	1.00[ASN][1000 genomes]
rs1371523	1.00[ASN][1000 genomes]
rs1371524	1.00[ASN][1000 genomes]
rs1371525	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1439877	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1439878	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1439912	0.93[ASN][1000 genomes]
rs1561569	1.00[ASN][1000 genomes]
rs1595765	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17264870	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1821997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837456	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2350560	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2350561	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180775	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180807	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62180809	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180813	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62180836	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6724481	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6734493	0.83[EUR][1000 genomes]
rs72911727	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7563498	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595927	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7596880	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893747	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977699	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533353	chr2:188498301-189024655	Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv875602	chr2:188923773-189016215	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv875603	chr2:188923773-189025977	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv584044	chr2:188928433-189016215	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1002714	chr2:188934297-189025084	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188939800-188944000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:188942400-188944600	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:188942800-188943600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:188942800-188943600	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr2:188943200-188943600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr2:188943200-188944400	Enhancers	HSMM	muscle
7	chr2:188943200-188944400	Enhancers	NHDF-Ad	bronchial
8	chr2:188943400-188944400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:188943400-188944400	Enhancers	GM12878-XiMat	blood
10	chr2:188943400-188944400	Enhancers	HSMMtube	muscle
11	chr2:188943400-188944600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:188943400-188944600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:188943400-188944600	Enhancers	Osteobl	bone

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