Variant report

Variant	rs13320527
Chromosome Location	chr3:178941323-178941324
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	chr3:178936118..178938279-chr3:178940553..178942291,2	K562	blood:
2	chr3:178884097..178886726-chr3:178940111..178942496,2	K562	blood:

Variant related genes	Relation type
ENSG00000121879	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10936993	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12486399	0.94[EUR][1000 genomes]
rs12497857	0.90[EUR][1000 genomes]
rs1517585	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2865084	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[EUR][1000 genomes]
rs28697961	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45455192	1.00[EUR][1000 genomes]
rs4854906	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4854940	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4854955	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4854976	0.94[EUR][1000 genomes]
rs4855094	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs4955793	1.00[GIH][hapmap];0.82[TSI][hapmap]
rs57779514	1.00[ASN][1000 genomes]
rs61404287	0.90[EUR][1000 genomes]
rs61796464	0.96[EUR][1000 genomes]
rs61796465	0.94[EUR][1000 genomes]
rs61796466	0.96[EUR][1000 genomes]
rs61796467	0.96[EUR][1000 genomes]
rs61798211	0.90[EUR][1000 genomes]
rs61798213	0.90[EUR][1000 genomes]
rs6443623	0.94[EUR][1000 genomes]
rs6791215	0.90[EUR][1000 genomes]
rs6804195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs73051979	0.96[EUR][1000 genomes]
rs73054091	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7374077	0.86[EUR][1000 genomes]
rs7615259	0.94[EUR][1000 genomes]
rs950486	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9812252	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9819654	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821850	1.00[ASN][1000 genomes]
rs9823044	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833206	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9860843	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9872959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878005	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv878038	chr3:178924867-178962897	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1005062	chr3:178929531-178942869	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv878039	chr3:178933363-178968568	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv965236	chr3:178938931-178955061	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178899200-178951800	Weak transcription	K562	blood
2	chr3:178906400-178962400	Weak transcription	HepG2	liver
3	chr3:178909000-178947000	Weak transcription	Ovary	ovary
4	chr3:178911200-178953400	Weak transcription	Gastric	stomach
5	chr3:178912400-178978600	Weak transcription	Right Ventricle	heart
6	chr3:178912600-178947800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:178913000-178948200	Weak transcription	Psoas Muscle	Psoas
8	chr3:178913200-178945200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:178913200-178947000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:178913200-178947000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:178913800-178954000	Weak transcription	Fetal Heart	heart
12	chr3:178913800-178969000	Weak transcription	Small Intestine	intestine
13	chr3:178914600-178945200	Weak transcription	HMEC	breast
14	chr3:178914800-178941400	Weak transcription	GM12878-XiMat	blood
15	chr3:178914800-178942800	Weak transcription	NH-A	brain
16	chr3:178914800-178948000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:178914800-178972800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:178915400-178946000	Weak transcription	Stomach Mucosa	stomach
19	chr3:178915400-178947000	Weak transcription	NHDF-Ad	bronchial
20	chr3:178915600-178947600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:178915800-178965200	Weak transcription	Hela-S3	cervix
22	chr3:178917400-178948400	Weak transcription	Esophagus	oesophagus
23	chr3:178917600-178953800	Weak transcription	Colonic Mucosa	Colon
24	chr3:178919800-178947000	Weak transcription	NHLF	lung
25	chr3:178920000-178947200	Weak transcription	Brain Angular Gyrus	brain
26	chr3:178920200-178947800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:178920200-178948800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:178920200-178952800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:178920200-178968400	Weak transcription	Spleen	Spleen
30	chr3:178921200-178948800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:178922200-178941400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:178922200-178945600	Weak transcription	HUVEC	blood vessel
33	chr3:178922600-178946200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:178924200-178948200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:178925800-178947600	Weak transcription	Aorta	Aorta
36	chr3:178925800-178951600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:178925800-178968200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:178925800-178968600	Weak transcription	Pancreas	Pancrea
39	chr3:178926400-178947600	Weak transcription	Brain Germinal Matrix	brain
40	chr3:178928400-178943200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:178928600-178944000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:178928600-178947000	Weak transcription	Fetal Brain Male	brain
43	chr3:178928600-178947600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:178928600-178962400	Weak transcription	Brain Substantia Nigra	brain
45	chr3:178928800-178948600	Weak transcription	Fetal Kidney	kidney
46	chr3:178928800-178953200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:178929000-178947000	Weak transcription	Osteobl	bone
48	chr3:178929200-178954000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:178929400-178948600	Weak transcription	Brain Anterior Caudate	brain
50	chr3:178929600-178947600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links