Variant report

Variant	rs6687774
Chromosome Location	chr1:185309133-185309134
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	EP300	chr1:185307755-185309220	GM12878	blood:	n/a	chr1:185308487-185308501 chr1:185308525-185308534

No.	Distal block	Cell Line	Cell type
1	chr1:185308094..185310941-chr1:185314344..185316672,2	MCF-7	breast:
2	chr1:185284682..185286513-chr1:185307599..185309324,2	MCF-7	breast:
3	chr1:185287917..185289698-chr1:185307396..185309858,2	K562	blood:
4	chr1:185299843..185302497-chr1:185306799..185309677,2	K562	blood:
5	chr1:185294862..185296528-chr1:185308605..185311231,2	K562	blood:

Variant related genes	Relation type
ENSG00000261024	TF binding region
ENSG00000261024	Chromatin interaction
ENSG00000116679	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10157232	0.83[EUR][1000 genomes]
rs10158623	0.89[EUR][1000 genomes]
rs10174	0.83[CHB][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10752947	0.80[MEX][hapmap]
rs10752948	0.85[CHD][hapmap]
rs10798004	0.93[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs10798006	0.92[EUR][1000 genomes]
rs10911702	0.83[CHB][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10911704	0.89[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10911707	1.00[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10911708	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12026391	0.83[CHB][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs12044943	0.84[EUR][1000 genomes]
rs17641003	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2152707	0.81[EUR][1000 genomes]
rs2224027	0.83[EUR][1000 genomes]
rs2281416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2378909	0.84[EUR][1000 genomes]
rs2378910	0.83[CHB][hapmap]
rs6656019	0.84[EUR][1000 genomes]
rs6665186	0.82[CHD][hapmap]
rs6682891	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs66845254	0.85[EUR][1000 genomes]
rs7123	0.89[CEU][hapmap];0.83[CHB][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs726567	0.94[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7512337	0.83[EUR][1000 genomes]
rs7537341	0.80[TSI][hapmap]
rs7545878	0.83[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs883753	0.83[CHB][hapmap]
rs997283	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	esv2756872	chr1:185293197-185345771	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv2758981	chr1:185293197-185345771	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6687774	TSEN15	cis	parietal	SCAN
rs6687774	NCRNA00272	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185304200-185310600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:185305200-185310200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:185305800-185309600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:185306400-185309800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:185306800-185311400	Weak transcription	Ovary	ovary
6	chr1:185307000-185309600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr1:185307000-185310200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr1:185307400-185309400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr1:185307400-185310200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:185307400-185310800	Enhancers	Primary T cells from cord blood	blood
11	chr1:185307400-185311000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:185307600-185309400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:185307600-185309800	Enhancers	Primary B cells from peripheral blood	blood
14	chr1:185307600-185310000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:185307800-185309400	Flanking Active TSS	Dnd41	blood
16	chr1:185307800-185309400	Flanking Active TSS	GM12878-XiMat	blood
17	chr1:185307800-185309600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:185307800-185309600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:185307800-185309600	Enhancers	Fetal Thymus	thymus
20	chr1:185307800-185310200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:185307800-185311000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:185308200-185310400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:185308600-185309400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr1:185308600-185309400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr1:185308800-185309400	Enhancers	Small Intestine	intestine
26	chr1:185308800-185309600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:185308800-185309600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:185308800-185309800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr1:185308800-185310400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:185308800-185311000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:185308800-185317600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:185309000-185309600	Enhancers	Primary hematopoietic stem cells	blood
33	chr1:185309000-185309600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:185309000-185310200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:185309000-185310800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr1:185309000-185310800	Enhancers	Primary B cells from cord blood	blood
37	chr1:185309000-185310800	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links