Variant report

Variant	rs209181
Chromosome Location	chr6:28792477-28792478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17375288	1.00[ASN][1000 genomes]
rs2765220	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3131344	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3132372	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs417919	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56271755	1.00[ASN][1000 genomes]
rs56678427	0.89[ASN][1000 genomes]
rs7739915	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9257182	0.81[AFR][1000 genomes]
rs9257190	0.83[AFR][1000 genomes]
rs9257226	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9468439	1.00[ASN][1000 genomes]
rs9468440	1.00[ASN][1000 genomes]
rs9500892	1.00[ASN][1000 genomes]
rs9501162	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs209181	ZNF323	cis	lymphoblastoid	seeQTL
rs209181	ZSCAN23	cis	parietal	SCAN
rs209181	LRRC16A	cis	parietal	SCAN
rs209181	ZNF187	cis	cerebellum	SCAN
rs209181	NKAPL	cis	parietal	SCAN
rs209181	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs209181	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs209181	ZNF323	cis	parietal	SCAN
rs209181	ZNF192	cis	cerebellum	SCAN
rs209181	HIST1H2BM	cis	cerebellum	SCAN
rs209181	ZKSCAN3	cis	cerebellum	SCAN
rs209181	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs209181	BTN3A3	cis	parietal	SCAN
rs209181	ZSCAN23	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28791200-28794000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:28792200-28792800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:28792200-28793400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:28792400-28792600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
5	chr6:28792400-28792600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
6	chr6:28792400-28792600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:28792400-28792800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:28792400-28792800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28792400-28792800	Bivalent Enhancer	HepG2	liver
10	chr6:28792400-28793000	Bivalent/Poised TSS	HMEC	breast
11	chr6:28792400-28793600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:28792400-28793600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr6:28792400-28793800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:28792400-28793800	Flanking Active TSS	K562	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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