Variant report

Variant	rs2004168
Chromosome Location	chr6:26843315-26843316
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10807012	0.95[ASN][1000 genomes]
rs10946853	0.84[ASN][1000 genomes]
rs10946859	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10946861	0.87[ASN][1000 genomes]
rs11754686	0.94[ASN][1000 genomes]
rs12191550	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2093303	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2636425	0.86[ASN][1000 genomes]
rs3933235	0.96[ASN][1000 genomes]
rs3933236	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4079824	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4236042	0.81[ASN][1000 genomes]
rs4521582	0.94[ASN][1000 genomes]
rs4713042	0.88[ASN][1000 genomes]
rs62400806	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6940771	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	esv2763937	chr6:26695219-26962934	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1800247	chr6:26695219-26970551	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2758038	chr6:26695219-27095714	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
5	esv2759410	chr6:26695219-27095714	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
6	esv2757158	chr6:26698480-26896889	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv33111	chr6:26703066-26946931	Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv883500	chr6:26706544-26922906	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv1810678	chr6:26718934-26946902	Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv1830610	chr6:26725354-26945518	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv883503	chr6:26781595-26915326	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv883504	chr6:26781595-26942027	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv830615	chr6:26789983-26922221	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv970088	chr6:26814715-26844272	Flanking Active TSS Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
15	nsv1029124	chr6:26825468-27109774	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	244 gene(s)	inside rSNPs	diseases
16	esv1848024	chr6:26828650-26946902	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	esv1801757	chr6:26832007-26947622	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	esv1811667	chr6:26832470-26972169	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv469610	chr6:26841083-26999230	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
20	nsv482509	chr6:26841083-26999230	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv471636	chr6:26841084-27038175	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2004168	BTN3A2	cis	lung	GTEx
rs2004168	RP11-457M11.5	cis	Artery Aorta	GTEx
rs2004168	RP11-457M11.5	cis	Muscle Skeletal	GTEx
rs2004168	RP11-457M11.5	cis	Skin Sun Exposed Lower leg	GTEx
rs2004168	RP11-457M11.5	cis	Whole Blood	GTEx
rs2004168	RP11-457M11.5	cis	lung	GTEx
rs2004168	RP11-457M11.5	cis	Esophagus Mucosa	GTEx
rs2004168	RP11-457M11.5	cis	Thyroid	GTEx
rs2004168	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs2004168	RP11-457M11.5	cis	Artery Tibial	GTEx
rs2004168	RP11-457M11.5	cis	Nerve Tibial	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26834600-26848800	Weak transcription	Liver	Liver
2	chr6:26838000-26866200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:26838400-26853400	Weak transcription	Adipose Nuclei	Adipose
4	chr6:26838800-26857600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:26839000-26850600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:26841400-26866200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links