Variant report

Variant	rs715217
Chromosome Location	chr20:1472408-1472409
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	POLR2A	chr20:1471263-1472481	HL-60	blood:	n/a	n/a
2	POLR2A	chr20:1471863-1472488	HUVEC	blood vessel:	n/a	n/a
3	SPI1	chr20:1472003-1472585	HL-60	blood:	n/a	chr20:1472270-1472283
4	SPI1	chr20:1471867-1473336	HL-60	blood:	n/a	chr20:1472270-1472283
5	POLR2A	chr20:1471682-1473023	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr20:1471849-1473033	HUVEC	blood vessel:	n/a	n/a
7	REST	chr20:1471798-1472418	HL-60	blood:	n/a	n/a
8	POLR2A	chr20:1471251-1472480	HL-60	blood:	n/a	n/a
9	GATA2	chr20:1472043-1472987	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
SIRPB2	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11697322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11697395	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11699494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13163	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16994239	1.00[CHB][hapmap]
rs16994549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16995146	1.00[CHB][hapmap]
rs16995310	1.00[CHB][hapmap]
rs16995332	1.00[CHB][hapmap]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1883933	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883936	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	1.00[CHB][hapmap]
rs2064645	1.00[CHB][hapmap]
rs2064646	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2249832	1.00[CHB][hapmap]
rs2250091	1.00[CHB][hapmap]
rs2253429	1.00[CHB][hapmap]
rs2253431	1.00[CHB][hapmap]
rs2253693	1.00[CHB][hapmap]
rs2253698	1.00[CHB][hapmap]
rs2256095	1.00[CHB][hapmap]
rs2256229	1.00[CHB][hapmap]
rs2256240	1.00[CHB][hapmap]
rs2256243	1.00[CHB][hapmap]
rs2256250	1.00[CHB][hapmap]
rs2256251	1.00[CHB][hapmap]
rs2263656	1.00[CHB][hapmap]
rs2873522	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4577347	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4813115	1.00[CHB][hapmap]
rs4814102	1.00[CHB][hapmap]
rs4814391	1.00[CHB][hapmap]
rs57094926	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap]
rs6033554	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6033660	1.00[CHB][hapmap]
rs6033871	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs6033896	1.00[CHB][hapmap]
rs6033911	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6033914	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6033918	0.84[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6033923	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033935	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs6033936	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6041689	1.00[CHB][hapmap]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6042506	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs6042550	1.00[CHB][hapmap]
rs6042568	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs6042574	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.80[YRI][hapmap]
rs6042578	1.00[CHB][hapmap]
rs6042585	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6042588	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6042647	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042676	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042682	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043372	1.00[CHB][hapmap]
rs6043374	1.00[CHB][hapmap]
rs60645920	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap]
rs6105101	1.00[CHB][hapmap]
rs6105437	1.00[CHB][hapmap]
rs6109437	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109511	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109522	1.00[CHB][hapmap]
rs6109740	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6109784	1.00[CHB][hapmap]
rs6109984	1.00[CHB][hapmap]
rs6109989	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6110189	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs6110193	1.00[CHB][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap]
rs6514337	1.00[CHB][hapmap]
rs6514364	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs66715055	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7271240	1.00[CHB][hapmap]
rs747611	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8117563	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8117719	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8118276	1.00[CHB][hapmap]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][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	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs715217	TMEM235	trans	brain	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1469200-1473000	Enhancers	HMEC	breast
2	chr20:1469800-1472600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr20:1469800-1474000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr20:1470000-1472600	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr20:1470000-1473200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:1470600-1473000	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr20:1471000-1472600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr20:1471000-1473000	Flanking Active TSS	HUVEC	blood vessel
9	chr20:1471200-1473000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr20:1471400-1473400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr20:1471600-1473000	Enhancers	Spleen	Spleen
12	chr20:1471600-1475800	Enhancers	Primary B cells from peripheral blood	blood
13	chr20:1471600-1478400	Weak transcription	NHEK	skin
14	chr20:1471600-1478800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr20:1471800-1472600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr20:1471800-1473000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr20:1471800-1474000	Enhancers	Fetal Thymus	thymus
18	chr20:1472000-1472600	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr20:1472000-1472800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr20:1472000-1473000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr20:1472200-1472800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr20:1472200-1473000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr20:1472200-1473200	Enhancers	Placenta	Placenta
24	chr20:1472200-1476000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr20:1472400-1472600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr20:1472400-1472800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr20:1472400-1473000	Enhancers	Adipose Nuclei	Adipose
28	chr20:1472400-1475600	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr20:1472400-1476000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links