Variant report

Variant	rs13207365
Chromosome Location	chr6:27030980-27030981
allele	C/T
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	GATA3	chr6:27030373-27031008	SK-N-SH	brain:	n/a	chr6:27030974-27030995

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26121476..26124237-chr6:27029296..27031595,2	K562	blood:

Variant related genes	Relation type
VN1R13P	TF binding region
ENSG00000180596	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10456349	0.88[ASN][1000 genomes]
rs10946896	0.88[ASN][1000 genomes]
rs10946899	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10946900	0.94[ASN][1000 genomes]
rs1102557	0.85[ASN][1000 genomes]
rs11961179	0.88[ASN][1000 genomes]
rs11961181	0.88[ASN][1000 genomes]
rs11962196	0.88[ASN][1000 genomes]
rs11966939	0.88[ASN][1000 genomes]
rs11969887	0.88[ASN][1000 genomes]
rs12190201	0.88[ASN][1000 genomes]
rs12190859	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12192049	0.94[ASN][1000 genomes]
rs12192320	0.94[ASN][1000 genomes]
rs12192446	0.94[ASN][1000 genomes]
rs12192502	0.88[ASN][1000 genomes]
rs12192766	0.94[ASN][1000 genomes]
rs12192793	0.85[ASN][1000 genomes]
rs12193463	0.88[ASN][1000 genomes]
rs12193511	0.88[ASN][1000 genomes]
rs12193820	0.94[ASN][1000 genomes]
rs12195041	0.88[ASN][1000 genomes]
rs12195144	0.94[ASN][1000 genomes]
rs12196889	0.82[ASN][1000 genomes]
rs12199218	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200985	0.88[ASN][1000 genomes]
rs12201498	0.94[ASN][1000 genomes]
rs12201774	0.94[ASN][1000 genomes]
rs12203145	0.88[ASN][1000 genomes]
rs12203454	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203728	0.94[ASN][1000 genomes]
rs12204280	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205921	0.94[ASN][1000 genomes]
rs12206996	0.94[ASN][1000 genomes]
rs12208039	0.88[ASN][1000 genomes]
rs12208534	0.94[ASN][1000 genomes]
rs12209393	0.94[ASN][1000 genomes]
rs12209429	0.94[ASN][1000 genomes]
rs12209456	0.94[ASN][1000 genomes]
rs12210905	0.85[ASN][1000 genomes]
rs12212317	0.88[ASN][1000 genomes]
rs12213361	0.91[ASN][1000 genomes]
rs12214848	0.94[ASN][1000 genomes]
rs12214930	0.94[ASN][1000 genomes]
rs12215241	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12215773	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17345718	0.88[ASN][1000 genomes]
rs3531	0.94[ASN][1000 genomes]
rs36048693	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3922717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3999221	0.88[ASN][1000 genomes]
rs41269245	0.94[ASN][1000 genomes]
rs4541737	0.88[ASN][1000 genomes]
rs4636015	0.94[ASN][1000 genomes]
rs6911234	0.94[ASN][1000 genomes]
rs6920115	0.88[ASN][1000 genomes]
rs6931711	0.85[ASN][1000 genomes]
rs6937764	0.88[ASN][1000 genomes]
rs6937955	0.88[ASN][1000 genomes]
rs6940638	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72838236	0.88[ASN][1000 genomes]
rs72838238	0.88[ASN][1000 genomes]
rs72838243	0.88[ASN][1000 genomes]
rs72838245	0.88[ASN][1000 genomes]
rs72838249	0.88[ASN][1000 genomes]
rs72838258	0.88[ASN][1000 genomes]
rs72838260	0.88[ASN][1000 genomes]
rs72838262	0.88[ASN][1000 genomes]
rs72838263	0.88[ASN][1000 genomes]
rs72838266	0.94[ASN][1000 genomes]
rs72838268	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72842200	0.94[ASN][1000 genomes]
rs72843607	0.94[ASN][1000 genomes]
rs72843608	0.94[ASN][1000 genomes]
rs72843609	0.91[ASN][1000 genomes]
rs72843611	0.91[ASN][1000 genomes]
rs72843613	0.91[ASN][1000 genomes]
rs72843615	0.85[ASN][1000 genomes]
rs72843619	0.82[ASN][1000 genomes]
rs7740207	0.88[ASN][1000 genomes]
rs7753123	0.88[ASN][1000 genomes]
rs7753284	0.88[ASN][1000 genomes]
rs7756481	0.94[ASN][1000 genomes]
rs7773336	0.88[ASN][1000 genomes]
rs9461316	0.88[ASN][1000 genomes]
rs9467939	0.82[ASN][1000 genomes]
rs9467940	0.82[ASN][1000 genomes]
rs9467942	0.88[ASN][1000 genomes]
rs9467965	0.88[ASN][1000 genomes]
rs9467971	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	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
5	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
6	nsv469625	chr6:26893739-27038175	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv482537	chr6:26893739-27038175	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv965631	chr6:27007405-27037069	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv3369822	chr6:27007480-27037513	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13207365	BTN2A2	Cis_1M	lymphoblastoid	RTeQTL
rs13207365	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27028000-27034200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:27028800-27032800	Weak transcription	K562	blood
3	chr6:27029600-27034000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:27029600-27034200	Weak transcription	HepG2	liver
5	chr6:27029600-27034400	Weak transcription	GM12878-XiMat	blood
6	chr6:27030000-27031400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:27030200-27031200	Enhancers	NHEK	skin
8	chr6:27030600-27034200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:27030800-27034200	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links