Variant report

Variant	rs2762060
Chromosome Location	chr13:50830002-50830003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50696545..50699318-chr13:50829348..50831026,2	MCF-7	breast:
2	chr13:50825700..50827613-chr13:50828901..50830460,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2762049	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812197	0.80[AMR][1000 genomes]
rs706606	0.92[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs806292	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs806293	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs806295	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs806296	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs806297	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs806316	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs806319	0.96[CEU][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs806321	0.92[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs806322	0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs806334	0.82[ASN][1000 genomes]
rs806349	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv900076	chr13:50710579-50912578	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv561631	chr13:50761619-50846748	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2762060	KCTD4	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50828000-50841400	Weak transcription	HepG2	liver
2	chr13:50828400-50831800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr13:50828600-50830200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr13:50829200-50830600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr13:50829200-50830800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr13:50829200-50833200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr13:50829200-50834200	Enhancers	Dnd41	blood
8	chr13:50829400-50830400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr13:50829400-50830600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr13:50829400-50830600	Enhancers	Fetal Thymus	thymus
11	chr13:50829600-50830600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr13:50829600-50830600	Enhancers	Thymus	Thymus
13	chr13:50829600-50832200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr13:50829800-50830400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr13:50829800-50830600	Enhancers	NHDF-Ad	bronchial
16	chr13:50829800-50831200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr13:50829800-50831800	Enhancers	Primary T cells from cord blood	blood
18	chr13:50830000-50830200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr13:50830000-50830400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr13:50830000-50831200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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