Variant report

Variant	rs2429549
Chromosome Location	chr17:38854406-38854407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38848480..38850542-chr17:38853579..38856285,2	K562	blood:
2	chr17:38798051..38800892-chr17:38851970..38854604,2	MCF-7	breast:
3	chr17:38801632..38805923-chr17:38849683..38856183,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073584	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1029792	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1048572	0.90[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs1048573	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs12943859	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2008469	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2014704	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2109223	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2159430	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2253717	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2315020	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2462962	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462963	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462964	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462970	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2469818	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3752026	0.95[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs4890093	0.90[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs4890119	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58630924	0.82[ASN][1000 genomes]
rs6503547	0.84[EUR][1000 genomes]
rs6503549	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7209467	0.95[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7209735	0.95[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7212255	0.91[ASN][1000 genomes]
rs7219483	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7223332	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7223354	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs726848	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs757411	0.88[GIH][hapmap]
rs758630	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8068721	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8076587	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs917593	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs917595	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9303294	0.86[YRI][hapmap]
rs9896791	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9900324	0.81[EUR][1000 genomes]
rs9906785	0.85[EUR][1000 genomes]
rs9915135	0.89[CEU][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2429549	TBCA	trans	cerebellum	SCAN
rs2429549	KRT222	cis	Nerve Tibial	GTEx
rs2429549	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs2429549	KRT32	cis	cerebellum	SCAN
rs2429549	KRT24	cis	Esophagus Mucosa	GTEx
rs2429549	CCL4	cis	parietal	SCAN
rs2429549	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs2429549	TADA2A	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38852000-38854600	Enhancers	Fetal Kidney	kidney
2	chr17:38853000-38859800	Weak transcription	Pancreas	Pancrea
3	chr17:38853200-38856200	Weak transcription	Gastric	stomach
4	chr17:38853200-38858400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr17:38853400-38855400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr17:38853400-38864000	Weak transcription	A549	lung
7	chr17:38853800-38859800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:38853800-38859800	Weak transcription	NHEK	skin
9	chr17:38853800-38864000	Weak transcription	Right Atrium	heart
10	chr17:38854000-38855400	Weak transcription	Placenta	Placenta
11	chr17:38854000-38855600	Weak transcription	Fetal Lung	lung
12	chr17:38854000-38858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:38854000-38858600	Weak transcription	Hela-S3	cervix
14	chr17:38854000-38861800	Weak transcription	HMEC	breast
15	chr17:38854000-38875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr17:38854400-38854600	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links