Variant report

Variant	rs56398778
Chromosome Location	chr1:86907262-86907263
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	chr1:86905357..86907939-chr1:86912947..86914769,2	K562	blood:
2	chr1:86906490..86909038-chr1:86911078..86912632,2	K562	blood:

Variant related genes	Relation type
ENSG00000137975	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10493793	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11805577	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17129186	1.00[EUR][1000 genomes]
rs28522658	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4647844	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4647848	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55719851	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56321760	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5744302	1.00[EUR][1000 genomes]
rs5744304	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5744314	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5744320	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5744324	1.00[EUR][1000 genomes]
rs5744335	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86896600-86914400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:86897200-86922600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:86897200-86922800	Strong transcription	HMEC	breast
4	chr1:86897400-86916000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:86902000-86913200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:86902400-86907400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:86903400-86926800	Weak transcription	Esophagus	oesophagus
8	chr1:86905800-86909400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:86906800-86908000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:86906800-86908000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr1:86906800-86908000	Enhancers	Dnd41	blood
12	chr1:86906800-86908200	Enhancers	Primary T cells from cord blood	blood
13	chr1:86906800-86908200	Enhancers	Thymus	Thymus
14	chr1:86906800-86909000	Enhancers	Fetal Thymus	thymus
15	chr1:86907000-86907600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:86907000-86907800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:86907000-86907800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:86907000-86907800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:86907000-86907800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:86907000-86908000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:86907000-86908000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:86907000-86908600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:86907000-86908800	Strong transcription	NHEK	skin
24	chr1:86907200-86907600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr1:86907200-86907600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr1:86907200-86907600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:86907200-86907600	Enhancers	Colonic Mucosa	Colon
28	chr1:86907200-86907800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links