Variant report

Variant	rs9817488
Chromosome Location	chr3:178973025-178973026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178971723..178975105-chr3:178977726..178980619,4	K562	blood:
2	chr3:178961023..178967533-chr3:178968774..178973213,9	K562	blood:
3	chr3:178969453..178970968-chr3:178972956..178974684,2	K562	blood:
4	chr3:178971723..178977145-chr3:178977567..178980865,6	K562	blood:
5	chr3:178970087..178973101-chr3:178973673..178977556,4	K562	blood:

Variant related genes	Relation type
ENSG00000240429	Chromatin interaction
ENSG00000171121	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs4854983	0.93[EUR][1000 genomes]
rs57134445	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73055889	0.91[EUR][1000 genomes]
rs7619958	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7624031	0.82[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7648422	1.00[ASW][hapmap];0.82[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9853868	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	esv1800747	chr3:178962897-178977074	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv1010137	chr3:178962897-179050787	Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
11	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9817488	KCNMB3	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178912400-178978600	Weak transcription	Right Ventricle	heart
2	chr3:178932200-178974000	Weak transcription	Lung	lung
3	chr3:178945800-178978400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:178948800-178978600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:178949000-178978200	Weak transcription	NHLF	lung
6	chr3:178949000-178978600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:178949000-178978600	Weak transcription	Ovary	ovary
8	chr3:178949000-178978800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:178949200-178978400	Weak transcription	Brain Anterior Caudate	brain
10	chr3:178949200-178978600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:178949200-178978600	Weak transcription	Osteobl	bone
12	chr3:178952000-178978400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:178952400-178978600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:178952600-178976600	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:178955000-178973800	Weak transcription	HSMMtube	muscle
16	chr3:178955200-178974400	Weak transcription	GM12878-XiMat	blood
17	chr3:178956200-178977000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:178959800-178978800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:178963200-178978200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:178963200-178978600	Weak transcription	Left Ventricle	heart
21	chr3:178963200-178978800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:178963800-178978800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:178966200-178978600	Weak transcription	HUVEC	blood vessel
24	chr3:178968800-178974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:178968800-178974800	Weak transcription	Adipose Nuclei	Adipose
26	chr3:178968800-178974800	Weak transcription	Spleen	Spleen
27	chr3:178968800-178978400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:178968800-178978600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:178969000-178975200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:178969200-178974800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:178969200-178978400	Weak transcription	Primary B cells from cord blood	blood
32	chr3:178969400-178974800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:178969400-178975600	Weak transcription	Gastric	stomach
34	chr3:178969400-178976600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:178969400-178978200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:178969600-178974000	Weak transcription	Pancreas	Pancrea
37	chr3:178969600-178978600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:178972000-178978800	Weak transcription	Small Intestine	intestine
39	chr3:178972200-178973400	Weak transcription	K562	blood
40	chr3:178972400-178973400	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links