Variant report

Variant	rs6993367
Chromosome Location	chr8:52870877-52870878
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	chr8:52870845..52873668-chr8:52875256..52877463,2	K562	blood:
2	chr8:52810400..52813872-chr8:52865354..52871657,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228801	Chromatin interaction
ENSG00000168300	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10086425	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10087958	0.83[EUR][1000 genomes]
rs10094042	0.84[ASN][1000 genomes]
rs10105030	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1013621	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs1013622	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11774370	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11781801	0.88[ASN][1000 genomes]
rs11786818	0.84[ASN][1000 genomes]
rs12335014	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs13256197	0.81[ASN][1000 genomes]
rs13263909	0.83[ASN][1000 genomes]
rs13267241	0.82[ASN][1000 genomes]
rs13275077	0.81[ASN][1000 genomes]
rs13276858	0.84[ASN][1000 genomes]
rs1467197	0.84[ASN][1000 genomes]
rs1515688	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1517306	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs16916858	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap]
rs2176121	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2395827	0.84[ASN][1000 genomes]
rs28619907	0.84[ASN][1000 genomes]
rs34619309	0.81[ASN][1000 genomes]
rs4565453	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4873611	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs6473660	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6473667	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6986544	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7001651	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7017926	0.81[ASN][1000 genomes]
rs7461587	0.88[ASN][1000 genomes]
rs7462096	0.81[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs7814421	0.89[ASW][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7827298	0.82[ASN][1000 genomes]
rs7835856	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7843189	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs877248	0.80[EUR][1000 genomes]
rs925762	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9298462	0.86[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap]

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	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6993367	PCMTD1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52867000-52873800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:52868200-52873600	Weak transcription	Primary B cells from cord blood	blood
3	chr8:52870000-52871000	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr8:52870200-52871000	Enhancers	HMEC	breast
5	chr8:52870200-52874200	Weak transcription	Fetal Brain Male	brain
6	chr8:52870400-52871000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr8:52870400-52871200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:52870600-52871400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr8:52870600-52871400	Enhancers	Pancreas	Pancrea
10	chr8:52870800-52871400	Enhancers	Placenta	Placenta
11	chr8:52870800-52873200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr8:52870800-52873800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links