Variant report

Variant	rs1883959
Chromosome Location	chr11:34234145-34234146
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	chr11:34213210..34216201-chr11:34233621..34235955,2	MCF-7	breast:
2	chr11:34224648..34227495-chr11:34231430..34234571,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1022722	0.98[ASN][1000 genomes]
rs11032552	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032554	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032555	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11032556	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11032557	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11032558	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11032559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11032561	0.87[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.80[ASN][1000 genomes]
rs11032562	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11604651	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12224748	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12271968	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12272398	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286749	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12417958	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12418582	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12420504	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2473900	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2611088	0.81[ASN][1000 genomes]
rs2611089	0.96[ASN][1000 genomes]
rs2746628	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2746629	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs55954105	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56126876	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7124297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7949361	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757435	chr11:34220504-34370236	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2759816	chr11:34220504-34370236	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv515783	chr11:34230517-34237292	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1883959	HIPK3	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34208200-34235200	Weak transcription	Adipose Nuclei	Adipose
2	chr11:34215000-34235800	Weak transcription	Brain Anterior Caudate	brain
3	chr11:34218800-34236600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:34219000-34240800	Weak transcription	Left Ventricle	heart
5	chr11:34219200-34236600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:34225800-34235000	Weak transcription	Liver	Liver
7	chr11:34226200-34236600	Weak transcription	Gastric	stomach
8	chr11:34226600-34244600	Weak transcription	Small Intestine	intestine
9	chr11:34227000-34235000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:34227000-34236400	Weak transcription	HSMM	muscle
11	chr11:34227000-34236400	Weak transcription	Osteobl	bone
12	chr11:34227000-34236600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:34227000-34244400	Weak transcription	Pancreas	Pancrea
14	chr11:34227400-34236600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr11:34228400-34236400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:34228600-34235400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:34228600-34236600	Weak transcription	Lung	lung
18	chr11:34228600-34236600	Weak transcription	Right Atrium	heart
19	chr11:34228800-34237200	Enhancers	HepG2	liver
20	chr11:34229000-34235000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:34229200-34235800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr11:34229200-34243000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr11:34229600-34234200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:34230200-34234200	Weak transcription	Fetal Muscle Leg	muscle
25	chr11:34230200-34235200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:34230200-34236600	Weak transcription	HSMMtube	muscle
27	chr11:34230400-34235000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:34230400-34236200	Weak transcription	NHEK	skin
29	chr11:34230600-34234400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:34230600-34235000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:34230600-34235200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:34230600-34235200	Weak transcription	Hela-S3	cervix
33	chr11:34230600-34235200	Weak transcription	NH-A	brain
34	chr11:34230600-34235600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:34230600-34236400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:34230600-34238600	Weak transcription	Psoas Muscle	Psoas
37	chr11:34230600-34244400	Weak transcription	Right Ventricle	heart
38	chr11:34230800-34236400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:34230800-34241000	Weak transcription	Placenta	Placenta
40	chr11:34232400-34236600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:34232400-34236600	Weak transcription	Brain Hippocampus Middle	brain
42	chr11:34232400-34241800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr11:34234000-34236000	Enhancers	Fetal Lung	lung
44	chr11:34234000-34236600	Enhancers	A549	lung
45	chr11:34234000-34237000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links