Variant report

Variant	rs2789972
Chromosome Location	chr1:223147668-223147669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223144142..223145952-chr1:223146468..223148708,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11487819	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2378617	0.88[EUR][1000 genomes]
rs2378618	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2378619	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609355	0.87[JPT][hapmap]
rs2609359	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2609366	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2609371	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789910	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2789924	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789929	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789931	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789933	0.91[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2789934	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2789937	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2789945	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2789953	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2789954	0.91[CEU][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2789957	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2789958	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34188904	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34620158	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34673329	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4317816	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4509582	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846783	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61837491	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67420224	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs728006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs946506	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv917330	chr1:223141547-223225893	Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2789972	ESRRG	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223140000-223147800	Weak transcription	Fetal Kidney	kidney
2	chr1:223143600-223149200	Weak transcription	Right Atrium	heart
3	chr1:223143800-223148000	Weak transcription	Ovary	ovary
4	chr1:223143800-223148800	Weak transcription	Fetal Lung	lung
5	chr1:223144200-223165400	Weak transcription	Left Ventricle	heart
6	chr1:223147000-223147800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:223147000-223147800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:223147000-223148200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:223147000-223148800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:223147000-223149800	Enhancers	Colon Smooth Muscle	Colon
11	chr1:223147000-223150200	Enhancers	Rectal Smooth Muscle	rectum
12	chr1:223147000-223150400	Enhancers	NHDF-Ad	bronchial
13	chr1:223147000-223150600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:223147000-223175800	Weak transcription	Aorta	Aorta
15	chr1:223147200-223147800	Enhancers	NHLF	lung
16	chr1:223147200-223148400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:223147200-223149800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:223147200-223150400	Enhancers	Osteobl	bone
19	chr1:223147400-223148200	Enhancers	Stomach Smooth Muscle	stomach
20	chr1:223147400-223148400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:223147400-223150000	Enhancers	NH-A	brain
22	chr1:223147400-223150400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr1:223147600-223148200	Enhancers	HSMM	muscle
24	chr1:223147600-223148200	Enhancers	HUVEC	blood vessel
25	chr1:223147600-223148600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:223147600-223150400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:223147600-223150600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links