Variant report

Variant	rs13026858
Chromosome Location	chr2:153270559-153270560
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153265041..153269898-chr2:153270458..153273464,4	K562	blood:
2	chr2:153262402..153264231-chr2:153268942..153273243,3	K562	blood:
3	chr2:153265232..153268503-chr2:153268822..153271827,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10179391	0.87[EUR][1000 genomes]
rs10203197	0.87[GIH][hapmap]
rs12991203	1.00[JPT][hapmap]
rs13003413	1.00[JPT][hapmap]
rs13007956	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs13029667	1.00[JPT][hapmap]
rs13398440	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13425532	1.00[CEU][hapmap]
rs2346199	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs35704894	0.83[ASN][1000 genomes]
rs6434003	0.87[EUR][1000 genomes]
rs6434017	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6707033	0.87[GIH][hapmap];0.87[EUR][1000 genomes]
rs6718081	0.87[EUR][1000 genomes]
rs6718584	0.87[EUR][1000 genomes]
rs6733002	0.87[GIH][hapmap]
rs6740909	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6741728	1.00[CEU][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv875291	chr2:153251742-153339823	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13026858	PAPSS2	trans	lymphoblastoid	seeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153247400-153277600	Weak transcription	Fetal Intestine Small	intestine
2	chr2:153264200-153288200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:153264400-153271200	Weak transcription	Aorta	Aorta
4	chr2:153264400-153274800	Enhancers	Brain Anterior Caudate	brain
5	chr2:153264400-153278000	Weak transcription	Fetal Kidney	kidney
6	chr2:153264600-153271800	Weak transcription	Right Atrium	heart
7	chr2:153264600-153277200	Enhancers	A549	lung
8	chr2:153265200-153274800	Weak transcription	Fetal Brain Male	brain
9	chr2:153265200-153278000	Weak transcription	Fetal Lung	lung
10	chr2:153265800-153272000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:153266000-153272800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:153266000-153278800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:153266200-153272600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:153266200-153279000	Enhancers	Brain Angular Gyrus	brain
15	chr2:153266600-153270800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:153267000-153272000	Enhancers	NHEK	skin
17	chr2:153267000-153277000	Weak transcription	NHLF	lung
18	chr2:153267000-153278800	Enhancers	Brain Cingulate Gyrus	brain
19	chr2:153267000-153279200	Enhancers	Brain Substantia Nigra	brain
20	chr2:153267200-153271000	Enhancers	HepG2	liver
21	chr2:153267200-153271200	Weak transcription	NH-A	brain
22	chr2:153267200-153271600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:153267200-153271800	Weak transcription	Gastric	stomach
24	chr2:153267200-153271800	Weak transcription	Lung	lung
25	chr2:153267400-153271000	Weak transcription	Left Ventricle	heart
26	chr2:153267600-153271600	Weak transcription	NHDF-Ad	bronchial
27	chr2:153267600-153271800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:153267600-153271800	Weak transcription	Right Ventricle	heart
29	chr2:153268000-153271000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:153268000-153271800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:153268000-153271800	Weak transcription	Osteobl	bone
32	chr2:153268200-153272000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:153268200-153277400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr2:153268400-153270800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:153268400-153271200	Weak transcription	Psoas Muscle	Psoas
36	chr2:153268400-153271400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:153268400-153272600	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:153268600-153271000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:153268600-153271000	Weak transcription	Stomach Mucosa	stomach
40	chr2:153268600-153272000	Weak transcription	Adipose Nuclei	Adipose
41	chr2:153268600-153277000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:153268800-153271000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:153268800-153271400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:153268800-153271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:153268800-153274000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:153269200-153270600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr2:153269200-153270800	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr2:153269200-153270800	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr2:153269200-153272200	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr2:153269400-153271600	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links