Variant report

Variant	rs2004990
Chromosome Location	chr3:112846690-112846691
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10934216	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10934217	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1574478	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1797608	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1797621	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1797622	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2017828	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2045687	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2045688	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2045690	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2045691	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2613919	0.85[ASN][1000 genomes]
rs2613920	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2613921	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2613922	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2613957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2700202	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2700203	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2700204	0.85[ASN][1000 genomes]
rs2700205	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2700206	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2700214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2926811	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2951458	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2951459	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2951460	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2951461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951462	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2951463	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3852010	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3852011	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4383482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4387939	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62262831	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6438129	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6438130	0.87[ASN][1000 genomes]
rs6807101	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7623035	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7632483	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7650532	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs878460	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9818149	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv877344	chr3:112789865-112854339	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv877345	chr3:112826253-112848851	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv518148	chr3:112845175-112846786	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112840600-112846800	Weak transcription	Fetal Stomach	stomach
2	chr3:112843200-112847200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:112843400-112847000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:112843400-112851200	Weak transcription	NHEK	skin
5	chr3:112843600-112847000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:112843800-112846800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:112843800-112847000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:112843800-112847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:112843800-112847000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:112844200-112847000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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