Variant report

Variant	rs2193476
Chromosome Location	chr2:56434331-56434332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10210479	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13026932	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1990757	0.82[CHB][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs214047	0.93[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2193473	0.81[CHB][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2193474	0.81[CHB][hapmap];0.82[AMR][1000 genomes]
rs2216323	0.81[CHB][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2869527	0.82[CHB][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2869528	0.82[CHB][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4672100	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6545558	0.86[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6719608	0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs979504	0.82[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs994297	0.85[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[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	esv2757799	chr2:56178439-56472394	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2759051	chr2:56178439-56472394	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
3	nsv874162	chr2:56255832-56480571	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874169	chr2:56383762-56473480	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2193476	TSPYL6	cis	parietal	SCAN
rs2193476	CCDC85A	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56420600-56443200	Weak transcription	Adipose Nuclei	Adipose
2	chr2:56421200-56437200	Weak transcription	Left Ventricle	heart
3	chr2:56423000-56443400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:56423200-56434600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:56429400-56437200	Strong transcription	HSMM	muscle
6	chr2:56430400-56436000	Weak transcription	Fetal Brain Male	brain
7	chr2:56430600-56434400	Weak transcription	HUVEC	blood vessel
8	chr2:56431000-56434600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:56432200-56434600	Enhancers	HMEC	breast
10	chr2:56432800-56434400	Weak transcription	HepG2	liver
11	chr2:56433200-56434800	Genic enhancers	Muscle Satellite Cultured Cells	--
12	chr2:56433200-56435200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr2:56433800-56434800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:56434000-56434800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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