Variant report

Variant	rs3788229
Chromosome Location	chr21:47335887-47335888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47325287..47328224-chr21:47334114..47336660,2	MCF-7	breast:
2	chr21:47290679..47292853-chr21:47334808..47337713,2	MCF-7	breast:
3	chr21:47172572..47175558-chr21:47335784..47338015,2	MCF-7	breast:
4	chr21:46960597..46962517-chr21:47334850..47337245,2	MCF-7	breast:
5	chr21:47335161..47336863-chr21:47355343..47357271,2	MCF-7	breast:
6	chr21:47326278..47326802-chr21:47335871..47336440,2	MCF-7	breast:
7	chr21:47286639..47289783-chr21:47334819..47337166,3	MCF-7	breast:
8	chr21:47329095..47331174-chr21:47334966..47337510,2	MCF-7	breast:
9	chr21:47334656..47336650-chr21:47402926..47405175,2	MCF-7	breast:
10	chr21:47319454..47322116-chr21:47334445..47336417,2	MCF-7	breast:
11	chr21:47267412..47269020-chr21:47335213..47337566,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000173638	Chromatin interaction
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10222081	0.94[ASN][1000 genomes]
rs10470261	0.94[ASN][1000 genomes]
rs13050871	0.90[CEU][hapmap]
rs16978692	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[ASN][1000 genomes]
rs1980979	0.90[CEU][hapmap]
rs2075887	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs2075907	0.98[ASN][1000 genomes]
rs2776402	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2839008	0.84[JPT][hapmap]
rs2839065	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2839066	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2839067	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2839068	0.94[ASN][1000 genomes]
rs2839069	0.94[ASN][1000 genomes]
rs2839071	0.84[ASN][1000 genomes]
rs3746990	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3746991	0.94[ASN][1000 genomes]
rs3788232	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3788235	0.96[ASN][1000 genomes]
rs3788237	0.90[CEU][hapmap]
rs3788239	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3788240	0.81[CEU][hapmap]
rs3788242	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs379493	0.88[ASN][1000 genomes]
rs379501	0.88[ASN][1000 genomes]
rs3827268	0.90[CEU][hapmap]
rs3827269	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[ASN][1000 genomes]
rs58139084	1.00[ASN][1000 genomes]
rs59605057	0.94[ASN][1000 genomes]
rs60282450	1.00[ASN][1000 genomes]
rs60911498	0.96[ASN][1000 genomes]
rs61639161	0.90[ASN][1000 genomes]
rs7276479	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7276791	0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7277199	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7278253	0.90[CEU][hapmap]
rs9306145	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs957347	0.84[ASN][1000 genomes]
rs9975850	1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[ASN][1000 genomes]
rs9975891	1.00[CEU][hapmap]
rs9977242	0.94[ASN][1000 genomes]
rs9983166	0.90[ASN][1000 genomes]
rs9983756	1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
11	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
12	nsv914082	chr21:47265786-47338007	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
14	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
15	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
16	nsv1062420	chr21:47311566-47347666	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
17	nsv1062386	chr21:47314890-47343364	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
18	nsv1061940	chr21:47317456-47343364	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
19	nsv1063852	chr21:47317456-47358709	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
20	nsv1060235	chr21:47317456-47360544	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47308000-47343000	Weak transcription	Right Atrium	heart
2	chr21:47321800-47337800	Weak transcription	Primary T cells from cord blood	blood
3	chr21:47330800-47342200	Weak transcription	Brain Hippocampus Middle	brain
4	chr21:47333600-47351600	Weak transcription	Gastric	stomach
5	chr21:47333800-47338800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr21:47334200-47336600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:47334200-47338000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr21:47334400-47340000	Weak transcription	Thymus	Thymus
9	chr21:47334800-47337000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:47335000-47337800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr21:47335200-47336800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr21:47335200-47337800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr21:47335400-47336800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr21:47335400-47337400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr21:47335600-47336400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr21:47335600-47336400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr21:47335600-47336400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr21:47335600-47336400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr21:47335600-47336400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr21:47335600-47336400	Enhancers	Fetal Lung	lung
21	chr21:47335600-47336600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr21:47335600-47336800	Enhancers	Primary hematopoietic stem cells	blood
23	chr21:47335600-47336800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:47335600-47336800	Enhancers	Fetal Thymus	thymus
25	chr21:47335600-47337000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr21:47335600-47337000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr21:47335600-47337800	Enhancers	Adipose Nuclei	Adipose
28	chr21:47335600-47338200	Enhancers	Spleen	Spleen
29	chr21:47335800-47336200	Weak transcription	HMEC	breast
30	chr21:47335800-47336400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr21:47335800-47336400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr21:47335800-47336600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr21:47335800-47336800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr21:47335800-47337000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links