Variant report

Variant	rs6672815
Chromosome Location	chr1:228784907-228784908
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	TBP	chr1:228782430-228785001	Hela-S3	cervix:	n/a	n/a
2	MAX	chr1:228784655-228784926	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:228782353-228785134	MCF10A-Er-Src	breast:	n/a	n/a
4	MAFK	chr1:228784807-228785381	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228782241..228785119-chr1:228785249..228788137,2	K562	blood:

Variant related genes	Relation type
ENSG00000206878	TF binding region
RNA5SP18	TF binding region
DUSP5P1	TF binding region
RNA5S17	TF binding region
ENSG00000183929	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10916348	0.90[ASW][hapmap];0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916349	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12040713	0.83[ASN][1000 genomes]
rs12045742	0.81[ASN][1000 genomes]
rs12046644	0.85[CHB][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.83[ASN][1000 genomes]
rs12047219	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12060147	0.85[EUR][1000 genomes]
rs12161195	0.80[ASN][1000 genomes]
rs12161347	0.80[ASN][1000 genomes]
rs1925715	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4344301	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs61827306	0.80[ASN][1000 genomes]
rs6426509	0.84[JPT][hapmap]
rs6658934	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6661618	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6681216	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs7355046	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7355153	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7546569	0.85[AMR][1000 genomes];0.92[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	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	esv1828070	chr1:228758016-228793246	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6672815	SNORD115-33	trans	cerebellum	SCAN
rs6672815	TP53BP2	cis	cerebellum	SCAN
rs6672815	FAM177B	cis	parietal	SCAN
rs6672815	CABC1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228782400-228785000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:228782400-228785000	Active TSS	Hela-S3	cervix
3	chr1:228784000-228785000	Bivalent Enhancer	Primary B cells from cord blood	blood
4	chr1:228784200-228785000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr1:228784200-228785000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr1:228784200-228785000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
7	chr1:228784200-228785000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:228784200-228785000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
9	chr1:228784200-228785000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:228784200-228785000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:228784200-228785000	Flanking Active TSS	NHEK	skin
12	chr1:228784200-228803000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:228784400-228785000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:228784400-228785000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr1:228784400-228785000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
16	chr1:228784400-228785000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
17	chr1:228784400-228785000	Bivalent Enhancer	HUVEC	blood vessel
18	chr1:228784400-228785200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
19	chr1:228784600-228785000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:228784600-228785000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:228784600-228785000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:228784600-228785000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:228784600-228785000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:228784600-228785000	Flanking Active TSS	HepG2	liver
25	chr1:228784600-228785200	Flanking Active TSS	A549	lung
26	chr1:228784800-228785000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr1:228784800-228785000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:228784800-228786000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:228784800-228786000	Weak transcription	Ovary	ovary
30	chr1:228784800-228786000	Weak transcription	Right Ventricle	heart
31	chr1:228784800-228787600	Weak transcription	Right Atrium	heart

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