Variant report

Variant	rs1568252
Chromosome Location	chr2:58169950-58169951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10188070	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs1040224	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1040225	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12622856	0.83[JPT][hapmap]
rs12713370	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1401100	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1518393	0.88[ASN][1000 genomes]
rs1518394	0.91[ASN][1000 genomes]
rs1518395	0.86[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1518399	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1568253	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1568254	0.90[ASN][1000 genomes]
rs2043890	0.83[JPT][hapmap]
rs2139053	0.94[ASN][1000 genomes]
rs2139054	0.88[ASN][1000 genomes]
rs2176546	0.88[ASN][1000 genomes]
rs2312141	0.88[ASN][1000 genomes]
rs2312147	0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2465804	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2678870	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2678880	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs2678881	0.82[ASN][1000 genomes]
rs2678889	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2678890	0.90[ASN][1000 genomes]
rs2678891	0.90[ASN][1000 genomes]
rs2678896	0.90[ASN][1000 genomes]
rs2678897	0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2678901	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2678903	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2678904	0.86[ASN][1000 genomes]
rs2678905	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2678906	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2678908	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2717001	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2717002	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2717004	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2717006	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2717007	0.86[ASN][1000 genomes]
rs2717015	0.87[ASN][1000 genomes]
rs2717019	1.00[JPT][hapmap]
rs2717023	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2717024	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2717027	0.96[ASN][1000 genomes]
rs2717031	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2717032	0.90[ASN][1000 genomes]
rs2717035	0.89[ASN][1000 genomes]
rs2717036	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2717040	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2717041	0.89[ASN][1000 genomes]
rs2717043	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2717056	0.80[ASN][1000 genomes]
rs28718871	0.90[ASN][1000 genomes]
rs6545677	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6732310	0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs893647	0.84[CEU][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs932188	0.81[ASN][1000 genomes]
rs966721	0.82[ASN][1000 genomes]
rs970941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[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	nsv874196	chr2:57946148-58220320	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010981	chr2:58013389-58205699	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv874200	chr2:58163178-58262016	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58169000-58170800	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr2:58169600-58170000	Enhancers	Brain Cingulate Gyrus	brain
3	chr2:58169600-58170400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:58169800-58170600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:58169800-58170800	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:58169800-58170800	Weak transcription	Brain Inferior Temporal Lobe	brain

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