Variant report

Variant	rs36069097
Chromosome Location	chr6:28601283-28601284
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	chr6:28582156..28586237-chr6:28601069..28603430,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCAND3-3	chr6:28601158-28601371	NONHSAT108475

Variant related genes	Relation type
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11963067	0.86[ASN][1000 genomes]
rs11965972	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11966966	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11967609	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11970339	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11970409	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13220637	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16894194	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16894197	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16901848	0.83[ASN][1000 genomes]
rs1884936	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1884937	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2394120	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2394121	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2893966	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34020953	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34177106	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34388845	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34556183	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35466817	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35546888	0.86[ASN][1000 genomes]
rs35778344	0.81[ASN][1000 genomes]
rs36103239	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4121091	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56389860	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61229539	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6923110	0.86[ASN][1000 genomes]
rs6941188	0.83[ASN][1000 genomes]
rs7741058	0.81[EUR][1000 genomes]
rs7742957	0.83[ASN][1000 genomes]
rs7767008	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7775683	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357070	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription 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	33 gene(s)	inside rSNPs	diseases
2	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs36069097	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs36069097	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs36069097	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28600600-28601600	Weak transcription	A549	lung
2	chr6:28600600-28601800	Weak transcription	HepG2	liver
3	chr6:28601000-28604000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:28601200-28601400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
5	chr6:28601200-28601400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:28601200-28601400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:28601200-28601400	Bivalent Enhancer	Aorta	Aorta
8	chr6:28601200-28601400	Bivalent/Poised TSS	Lung	lung
9	chr6:28601200-28601400	ZNF genes & repeats	Pancreas	Pancrea
10	chr6:28601200-28601600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:28601200-28601600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
12	chr6:28601200-28601800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:28601200-28602200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr6:28601200-28602200	Enhancers	Fetal Kidney	kidney
15	chr6:28601200-28603200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr6:28601200-28603800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:28601200-28603800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr6:28601200-28604000	Active TSS	H9 Cell Line	embryonic stem cell

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