Variant report

Variant	rs6681870
Chromosome Location	chr1:85038958-85038959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
2	chr1:85038587..85040484-chr1:85154316..85157145,3	K562	blood:
3	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:
4	chr1:84943703..84948095-chr1:85037647..85043843,8	K562	blood:
5	chr1:85037440..85039387-chr1:85215533..85217595,2	K562	blood:
6	chr1:84943714..84946459-chr1:85038706..85040687,2	K562	blood:
7	chr1:84971888..84972401-chr1:85038907..85039676,2	Hela-S3	cervix:
8	chr1:84981895..84983594-chr1:85038759..85040423,2	K562	blood:
9	chr1:85038555..85039249-chr1:209979030..209979922,2	HCT-116	colon:
10	chr1:84953201..84955322-chr1:85035250..85039258,3	K562	blood:
11	chr1:85035171..85039138-chr1:85044940..85048929,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117595	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000117133	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000122432	Chromatin interaction

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

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

rs_ID	r²[population]
rs1043493	0.91[GIH][hapmap]
rs10493753	0.83[GIH][hapmap]
rs11164009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1156435	0.91[GIH][hapmap]
rs12084159	0.94[EUR][1000 genomes]
rs17099163	0.91[GIH][hapmap]
rs17110157	0.91[GIH][hapmap]
rs17111308	0.91[GIH][hapmap]
rs17111464	0.91[GIH][hapmap]
rs57674741	0.83[EUR][1000 genomes]
rs58537059	0.83[EUR][1000 genomes]
rs6679620	0.94[EUR][1000 genomes]
rs6692607	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7533783	0.83[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	nsv1000325	chr1:85032605-85100748	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85008800-85039000	Weak transcription	Fetal Brain Male	brain
2	chr1:85014800-85039600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:85017400-85039600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:85028800-85039600	Weak transcription	Gastric	stomach
5	chr1:85034600-85039400	Weak transcription	Esophagus	oesophagus
6	chr1:85035400-85039200	Weak transcription	Lung	lung
7	chr1:85035400-85039400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:85035400-85039400	Weak transcription	Pancreas	Pancrea
9	chr1:85036800-85039200	Weak transcription	Ovary	ovary
10	chr1:85037400-85041200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:85037600-85039600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:85037800-85041200	Active TSS	GM12878-XiMat	blood
13	chr1:85038000-85039600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr1:85038200-85039600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr1:85038200-85039600	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr1:85038200-85039800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr1:85038200-85040000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:85038200-85041000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:85038400-85039000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:85038400-85039000	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr1:85038400-85039000	Enhancers	Fetal Thymus	thymus
22	chr1:85038400-85039000	Enhancers	Left Ventricle	heart
23	chr1:85038400-85039200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:85038400-85039200	Flanking Active TSS	Liver	Liver
25	chr1:85038400-85039200	Enhancers	Small Intestine	intestine
26	chr1:85038400-85039200	Flanking Active TSS	NHEK	skin
27	chr1:85038400-85039400	Enhancers	Placenta	Placenta
28	chr1:85038400-85039600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr1:85038400-85039600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr1:85038400-85039600	Flanking Active TSS	Dnd41	blood
31	chr1:85038400-85039800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:85038400-85039800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr1:85038400-85039800	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr1:85038400-85039800	Flanking Active TSS	Osteobl	bone
35	chr1:85038400-85040000	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr1:85038400-85040600	Active TSS	Colonic Mucosa	Colon
37	chr1:85038400-85040800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:85038600-85039000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:85038600-85039000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:85038600-85039000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr1:85038600-85039000	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr1:85038600-85039000	Flanking Active TSS	NHLF	lung
43	chr1:85038600-85039200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:85038600-85039200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr1:85038600-85039200	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr1:85038600-85039200	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr1:85038600-85039200	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr1:85038600-85039200	Enhancers	Stomach Mucosa	stomach
49	chr1:85038600-85039400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr1:85038600-85039400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links