Variant report

Variant	rs12505990
Chromosome Location	chr4:62140177-62140178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10010876	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10018853	0.91[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs10033220	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11723103	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11731649	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12331903	0.82[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs12505585	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12508911	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12511914	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13127903	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13140257	0.84[ASN][1000 genomes]
rs1505664	1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1505682	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1505685	0.91[CEU][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17219732	0.82[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2342455	0.85[ASN][1000 genomes]
rs2342486	0.82[ASN][1000 genomes]
rs28634991	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35289145	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4860406	0.87[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs67050759	0.87[ASN][1000 genomes]
rs950867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972616	0.85[ASN][1000 genomes]
rs974538	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs9998310	0.96[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879075	chr4:62124531-62354791	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62128200-62143600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:62135800-62140400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:62136000-62151200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:62136200-62147200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:62138200-62140200	Enhancers	Primary hematopoietic stem cells	blood
6	chr4:62138400-62141000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr4:62139400-62140200	Weak transcription	Fetal Lung	lung
8	chr4:62139400-62140400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:62139400-62141000	Weak transcription	Brain Anterior Caudate	brain
10	chr4:62139600-62140400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:62140000-62140200	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr4:62140000-62140600	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:62140000-62140800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:62140000-62141000	Enhancers	Brain Substantia Nigra	brain
15	chr4:62140000-62141200	Weak transcription	Brain Angular Gyrus	brain

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