Variant report

Variant	rs572708
Chromosome Location	chr6:33667857-33667858
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	RAD21	chr6:33667793-33668807	SK-N-SH	brain:	n/a	chr6:33668463-33668476 chr6:33668413-33668432 chr6:33668465-33668475
2	POLR2A	chr6:33667752-33667864	A549	lung:	n/a	n/a
3	SMC3	chr6:33667735-33668829	SK-N-SH	brain:	n/a	chr6:33668465-33668475 chr6:33668417-33668431
4	NFIC	chr6:33667631-33668306	GM12878	blood:	n/a	n/a
5	EBF1	chr6:33667602-33667997	GM12878	blood:	n/a	chr6:33667801-33667811 chr6:33667800-33667811 chr6:33667802-33667811 chr6:33667669-33667679
6	EBF1	chr6:33667603-33667882	GM12878	blood:	n/a	chr6:33667801-33667811 chr6:33667800-33667811 chr6:33667802-33667811 chr6:33667669-33667679
7	POLR2A	chr6:33667851-33668907	PANC-1	pancreas:	n/a	n/a
8	RUNX3	chr6:33667573-33667954	GM12878	blood:	n/a	chr6:33667787-33667802

No.	Distal block	Cell Line	Cell type
1	chr6:33590320..33593181-chr6:33667665..33670096,2	MCF-7	breast:
2	chr6:33243707..33246364-chr6:33666916..33668671,2	MCF-7	breast:
3	chr6:33557862..33560664-chr6:33667390..33670226,3	MCF-7	breast:
4	chr6:33557322..33558111-chr6:33667371..33668903,6	MCF-7	breast:
5	chr6:33553081..33555328-chr6:33667772..33669168,10	K562	blood:
6	chr6:33667241..33669923-chr6:33710850..33712681,2	K562	blood:
7	chr6:33556676..33558804-chr6:33667221..33669587,2	K562	blood:
8	chr6:33667395..33669385-chr6:33670170..33673083,3	MCF-7	breast:

Variant related genes	Relation type
UQCC2	TF binding region
ENSG00000269490	TF binding region
ENSG00000235863	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2094349	1.00[CHB][hapmap]
rs4711333	1.00[CHD][hapmap]
rs4713647	1.00[CHD][hapmap]
rs485623	1.00[CHD][hapmap]
rs525623	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557559	1.00[CHD][hapmap]
rs559290	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs560218	1.00[CHD][hapmap]
rs594223	0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs649775	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs653536	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6929190	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931761	1.00[CHB][hapmap]
rs7752152	1.00[CHB][hapmap]
rs7757722	1.00[CHD][hapmap]
rs791900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461902	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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs572708	PPIL1	cis	parietal	SCAN
rs572708	C6orf126	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33621400-33672600	Strong transcription	Dnd41	blood
2	chr6:33640000-33669200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:33641400-33668000	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr6:33650400-33669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:33650600-33668000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:33653000-33668600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:33659400-33668400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr6:33660200-33669400	Strong transcription	HepG2	liver
9	chr6:33661400-33669200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:33661600-33668600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr6:33661600-33668800	Genic enhancers	NHEK	skin
12	chr6:33661800-33675800	Weak transcription	Ovary	ovary
13	chr6:33662800-33669600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:33663000-33668000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:33663000-33669000	Strong transcription	K562	blood
16	chr6:33663000-33678200	Weak transcription	Fetal Kidney	kidney
17	chr6:33663200-33668200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:33663600-33668400	Strong transcription	Liver	Liver
19	chr6:33663600-33669600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:33663800-33668600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:33663800-33678600	Weak transcription	Small Intestine	intestine
22	chr6:33664200-33668000	Strong transcription	Fetal Intestine Small	intestine
23	chr6:33664600-33678000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:33664800-33668400	Strong transcription	Fetal Intestine Large	intestine
25	chr6:33664800-33669400	Strong transcription	Placenta	Placenta
26	chr6:33664800-33676200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:33665000-33668400	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr6:33665000-33668600	Enhancers	Primary B cells from cord blood	blood
29	chr6:33665000-33668800	Genic enhancers	GM12878-XiMat	blood
30	chr6:33665200-33668800	Genic enhancers	Primary T cells from cord blood	blood
31	chr6:33665200-33668800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:33665200-33669000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:33665200-33678000	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:33665200-33678200	Weak transcription	Brain Substantia Nigra	brain
35	chr6:33665200-33678600	Weak transcription	Aorta	Aorta
36	chr6:33665400-33668000	Strong transcription	A549	lung
37	chr6:33665400-33668000	Strong transcription	NHDF-Ad	bronchial
38	chr6:33665400-33668200	Strong transcription	HSMM	muscle
39	chr6:33665400-33668400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:33665400-33669400	Strong transcription	Osteobl	bone
41	chr6:33665400-33669600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr6:33665400-33669800	Strong transcription	NHLF	lung
43	chr6:33665400-33670200	Weak transcription	Fetal Brain Male	brain
44	chr6:33665400-33672200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:33665400-33677800	Weak transcription	Stomach Mucosa	stomach
46	chr6:33665600-33668000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:33665600-33669600	Strong transcription	Hela-S3	cervix
48	chr6:33665600-33678200	Weak transcription	NH-A	brain
49	chr6:33665600-33678400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:33665800-33669400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links