Variant report

Variant	rs10494259
Chromosome Location	chr1:149939137-149939138
allele	C/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:149932187..149934203-chr1:149937338..149939359,2	MCF-7	breast:
2	chr1:149912344..149915239-chr1:149936515..149940738,3	MCF-7	breast:
3	chr1:149936950..149941153-chr1:149941683..149945948,4	K562	blood:
4	chr1:149909949..149911935-chr1:149937678..149940090,2	MCF-7	breast:
5	chr1:149855178..149861916-chr1:149928782..149939792,19	MCF-7	breast:
6	chr1:149937397..149939684-chr1:150018242..150019838,2	MCF-7	breast:
7	chr1:149897715..149899381-chr1:149937367..149939579,2	MCF-7	breast:
8	chr1:149939082..149940718-chr1:149951900..149953765,2	K562	blood:
9	chr1:149938841..149939614-chr1:150022722..150023249,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184260	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10494261	0.92[ASW][hapmap];0.88[MKK][hapmap]
rs1061955	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11205308	0.92[ASW][hapmap];0.91[MKK][hapmap]
rs11205313	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs11205314	1.00[AMR][1000 genomes]
rs12022928	0.90[YRI][hapmap]
rs12060171	1.00[AMR][1000 genomes]
rs12060830	1.00[ASW][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap]
rs12064434	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082035	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091025	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs12091858	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs12091904	1.00[AMR][1000 genomes]
rs16833063	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833149	0.90[YRI][hapmap]
rs16833175	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs16833178	0.92[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs16838432	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4279885	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58342123	1.00[AMR][1000 genomes]
rs74126211	1.00[AMR][1000 genomes]
rs7517085	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9804143	0.85[ASW][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9988489	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][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	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149909400-149947000	Weak transcription	Fetal Brain Male	brain
2	chr1:149912600-149941600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:149921200-149942600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:149922400-149951600	Weak transcription	Small Intestine	intestine
5	chr1:149929400-149940000	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:149929400-149948400	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr1:149929600-149940200	Strong transcription	HUVEC	blood vessel
8	chr1:149929600-149950200	Strong transcription	Osteobl	bone
9	chr1:149930000-149940000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr1:149930400-149943600	Strong transcription	Fetal Stomach	stomach
11	chr1:149930600-149939800	Strong transcription	NHDF-Ad	bronchial
12	chr1:149930800-149959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:149931800-149946200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:149931800-149949600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:149931800-149949800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:149932000-149949200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:149932000-149949600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:149932200-149942600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:149933000-149939800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:149933000-149945400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:149933200-149947000	Strong transcription	Fetal Intestine Large	intestine
22	chr1:149933200-149949600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:149934200-149958000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:149934400-149940800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:149934400-149949600	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:149934600-149940000	Strong transcription	Placenta	Placenta
27	chr1:149934600-149941200	Weak transcription	Fetal Thymus	thymus
28	chr1:149934600-149947600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr1:149934600-149949600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:149934600-149949600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:149934800-149941600	Strong transcription	GM12878-XiMat	blood
32	chr1:149935200-149939400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:149935200-149939600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr1:149935200-149939800	Strong transcription	Rectal Smooth Muscle	rectum
35	chr1:149935400-149939400	Strong transcription	Brain Germinal Matrix	brain
36	chr1:149935600-149939800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:149935600-149950400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:149935800-149939400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:149935800-149939400	Strong transcription	Colon Smooth Muscle	Colon
40	chr1:149935800-149939400	Strong transcription	Psoas Muscle	Psoas
41	chr1:149935800-149939600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:149935800-149939600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:149935800-149939800	Strong transcription	Right Ventricle	heart
44	chr1:149935800-149940000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr1:149935800-149940000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:149935800-149940000	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:149935800-149941400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:149935800-149947400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:149935800-149948000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:149935800-149948200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links