Variant report

Variant	rs231023
Chromosome Location	chr17:15158775-15158776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15154649..15157419-chr17:15157540..15162043,4	MCF-7	breast:
2	chr17:15158560..15160723-chr17:15400595..15402410,2	K562	blood:

Variant related genes	Relation type
ENSG00000265110	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs230911	0.81[CEU][hapmap]
rs230950	0.83[MKK][hapmap]
rs231018	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs231020	0.96[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs231024	0.85[CEU][hapmap]
rs231025	1.00[CEU][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs231027	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs231028	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs231029	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs231030	0.80[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55568	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs66507245	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066329	chr17:14983674-15294071	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543212	chr17:14983674-15294071	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv530760	chr17:15152791-15162532	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs231023	PIGL	cis	cerebellum	SCAN
rs231023	ADORA2B	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15132200-15158800	Weak transcription	Hela-S3	cervix
2	chr17:15135800-15160200	Weak transcription	Pancreas	Pancrea
3	chr17:15139800-15160200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr17:15142600-15159000	Weak transcription	Fetal Kidney	kidney
5	chr17:15142600-15159000	Weak transcription	NH-A	brain
6	chr17:15142800-15159200	Weak transcription	Fetal Brain Male	brain
7	chr17:15146800-15160400	Strong transcription	A549	lung
8	chr17:15148000-15159000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:15148200-15159000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr17:15148200-15160400	Strong transcription	Fetal Stomach	stomach
11	chr17:15149800-15160200	Genic enhancers	Brain Hippocampus Middle	brain
12	chr17:15150800-15159400	Genic enhancers	Brain Cingulate Gyrus	brain
13	chr17:15150800-15160200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr17:15150800-15160200	Genic enhancers	Adipose Nuclei	Adipose
15	chr17:15151000-15160000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr17:15151200-15159200	Genic enhancers	Brain Anterior Caudate	brain
17	chr17:15151400-15160000	Strong transcription	HUVEC	blood vessel
18	chr17:15151400-15160000	Weak transcription	K562	blood
19	chr17:15151400-15160200	Strong transcription	HSMM	muscle
20	chr17:15151400-15160200	Genic enhancers	NHDF-Ad	bronchial
21	chr17:15151600-15159000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:15151600-15159200	Strong transcription	NHLF	lung
23	chr17:15151800-15158800	Strong transcription	Osteobl	bone
24	chr17:15151800-15159000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:15151800-15159400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr17:15151800-15160400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr17:15152000-15160200	Genic enhancers	Colon Smooth Muscle	Colon
28	chr17:15152200-15158800	Weak transcription	HMEC	breast
29	chr17:15152200-15160400	Strong transcription	Fetal Intestine Large	intestine
30	chr17:15153200-15159000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr17:15153400-15159200	Strong transcription	Aorta	Aorta
32	chr17:15153600-15158800	Genic enhancers	Stomach Smooth Muscle	stomach
33	chr17:15153600-15159000	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr17:15153800-15160200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr17:15154000-15159200	Strong transcription	HSMMtube	muscle
36	chr17:15154400-15159800	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr17:15154600-15160200	Weak transcription	Spleen	Spleen
38	chr17:15154800-15159000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr17:15154800-15159400	Strong transcription	Fetal Lung	lung
40	chr17:15155200-15161600	Weak transcription	Esophagus	oesophagus
41	chr17:15155400-15160400	Strong transcription	Fetal Intestine Small	intestine
42	chr17:15156000-15160600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr17:15156400-15159000	Strong transcription	Ovary	ovary
44	chr17:15156400-15159000	Weak transcription	Right Atrium	heart
45	chr17:15156400-15160000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr17:15156800-15159400	Genic enhancers	Brain Angular Gyrus	brain
47	chr17:15156800-15159400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr17:15157000-15159200	Genic enhancers	Rectal Smooth Muscle	rectum
49	chr17:15157000-15160000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr17:15157200-15159400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links