Variant report

Variant	rs6518217
Chromosome Location	chr21:46610915-46610916
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46610725..46612939-chr21:46706315..46708267,2	K562	blood:
2	chr21:46610563..46614105-chr21:46617394..46620381,3	K562	blood:
3	chr14:80314394..80315306-chr21:46610859..46611401,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215447	Chromatin interaction
ENSG00000186866	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10222166	1.00[CEU][hapmap]
rs11911460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12483288	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12627065	0.94[ASN][1000 genomes]
rs12627151	0.94[ASN][1000 genomes]
rs13433524	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1556318	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556319	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17004743	0.94[ASN][1000 genomes]
rs17004748	0.94[ASN][1000 genomes]
rs2838801	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838802	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838809	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838810	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838811	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838812	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838814	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838816	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372549	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs3746976	0.82[ASN][1000 genomes]
rs3788169	0.94[ASN][1000 genomes]
rs3788170	0.90[ASN][1000 genomes]
rs3788171	0.89[ASN][1000 genomes]
rs3788181	0.96[ASN][1000 genomes]
rs398023	0.94[ASN][1000 genomes]
rs6518215	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6518216	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6518218	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66664884	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66837495	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277143	1.00[CEU][hapmap]
rs7279808	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7283317	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8129624	0.94[ASN][1000 genomes]
rs8130097	0.94[ASN][1000 genomes]
rs8130862	0.97[ASN][1000 genomes]
rs8132646	1.00[ASN][1000 genomes]
rs8134382	1.00[ASN][1000 genomes]
rs914211	0.82[CEU][hapmap]
rs9653788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9978240	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9978543	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
12	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers 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	53 gene(s)	inside rSNPs	diseases
13	nsv916959	chr21:46585681-46831845	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
14	nsv1063721	chr21:46610599-46907894	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46589000-46646000	Weak transcription	Colonic Mucosa	Colon
2	chr21:46604600-46615000	Strong transcription	Skeletal Muscle Female	skeletal muscle
3	chr21:46604800-46611400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr21:46604800-46618200	Strong transcription	Hela-S3	cervix
5	chr21:46605200-46620000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:46605800-46611000	ZNF genes & repeats	Fetal Lung	lung
7	chr21:46605800-46612800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr21:46605800-46613000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr21:46606000-46611000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
10	chr21:46606000-46611200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr21:46606000-46612200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr21:46606000-46624400	Weak transcription	Esophagus	oesophagus
13	chr21:46606000-46630600	Weak transcription	Pancreas	Pancrea
14	chr21:46606200-46611000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
15	chr21:46606200-46611000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
16	chr21:46606400-46619200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr21:46606600-46611000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
18	chr21:46606600-46622200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr21:46606800-46624400	Weak transcription	Ovary	ovary
20	chr21:46606800-46624400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr21:46606800-46628400	Weak transcription	NH-A	brain
22	chr21:46606800-46640800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr21:46607000-46622400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr21:46607400-46611400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr21:46607600-46611000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr21:46607600-46628600	Weak transcription	Osteobl	bone
27	chr21:46607800-46619200	Weak transcription	HMEC	breast
28	chr21:46608000-46619600	Strong transcription	HSMM	muscle
29	chr21:46608400-46618000	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr21:46608400-46618200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr21:46608800-46611000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr21:46609000-46624400	Weak transcription	Thymus	Thymus
33	chr21:46609000-46624600	Weak transcription	Placenta	Placenta
34	chr21:46609000-46630600	Weak transcription	Fetal Thymus	thymus
35	chr21:46609000-46630800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr21:46609200-46611400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr21:46609200-46615200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr21:46609400-46611400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr21:46609600-46611000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr21:46609600-46634600	Weak transcription	Fetal Heart	heart
41	chr21:46609800-46611000	Strong transcription	Liver	Liver
42	chr21:46609800-46611000	Strong transcription	Fetal Brain Male	brain
43	chr21:46610000-46612800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr21:46610000-46634800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr21:46610000-46644800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr21:46610200-46611400	Strong transcription	Adipose Nuclei	Adipose
47	chr21:46610200-46613400	Strong transcription	Primary T cells from cord blood	blood
48	chr21:46610200-46613400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr21:46610200-46623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr21:46610200-46634400	Weak transcription	Psoas Muscle	Psoas

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