Variant report

Variant	rs7573258
Chromosome Location	chr2:211438396-211438397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:211435999-211442943	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:211437973-211438846	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
CPS1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10165443	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10184633	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10191702	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1047883	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10932339	0.81[JPT][hapmap]
rs12694201	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12694202	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12694203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12694204	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1509820	0.81[JPT][hapmap]
rs2007748	0.81[JPT][hapmap]
rs2229589	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2287599	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs2287603	0.82[JPT][hapmap]
rs2302910	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2370997	0.80[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2370998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2371000	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2371001	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs2371002	0.96[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs4312427	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4396646	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4399666	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6435578	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714124	0.86[GIH][hapmap];0.81[TSI][hapmap]
rs6721477	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6734696	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7580046	0.81[JPT][hapmap]
rs7582951	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7583822	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7593211	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7598448	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7603241	0.81[JPT][hapmap]

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	esv3398091	chr2:211315261-211634200	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7573258	CPS1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211418600-211443200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:211433000-211438400	Genic enhancers	Liver	Liver
3	chr2:211433200-211442200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:211433200-211442200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:211434000-211442000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:211434400-211439800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:211435200-211448200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:211435800-211447400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:211436600-211440200	Genic enhancers	Fetal Intestine Large	intestine
10	chr2:211436600-211440200	Enhancers	Fetal Intestine Small	intestine
11	chr2:211437600-211439400	Strong transcription	Duodenum Mucosa	Duodenum
12	chr2:211437800-211438400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:211438000-211438400	Enhancers	Fetal Kidney	kidney
14	chr2:211438000-211438400	Enhancers	Small Intestine	intestine
15	chr2:211438000-211446200	Strong transcription	Hela-S3	cervix

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