Variant report

Variant	rs16854861
Chromosome Location	chr1:179845607-179845608
allele	C/G
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	chr1:179843719..179847778-chr1:180121939..180127812,8	K562	blood:
2	chr1:179845348..179847730-chr1:179923811..179926342,3	MCF-7	breast:
3	chr1:179844647..179846808-chr1:180163421..180165631,2	K562	blood:
4	chr1:179842979..179846933-chr1:179922588..179926684,5	K562	blood:
5	chr1:179844379..179846987-chr1:180122185..180123975,2	MCF-7	breast:
6	chr1:179834118..179836947-chr1:179843310..179847312,3	MCF-7	breast:
7	chr1:179845220..179846816-chr1:179967799..179969791,2	MCF-7	breast:
8	chr1:179832603..179840385-chr1:179843229..179848672,10	MCF-7	breast:
9	chr1:179845449..179848601-chr1:179867688..179872232,4	K562	blood:
10	chr1:179844894..179847778-chr1:180122782..180124340,2	K562	blood:
11	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction
ENSG00000264916	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000258664	Chromatin interaction
ENSG00000260360	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10436866	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12239940	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13374504	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854828	0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854841	0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs16854843	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854853	0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854895	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854908	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854921	0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854935	0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16854952	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs56725488	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59284984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59961638	0.89[AFR][1000 genomes];1.00[AMR][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	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS 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	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv519273	chr1:179831248-179847877	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179835000-179846400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:179835000-179846400	Weak transcription	Spleen	Spleen
3	chr1:179835400-179846000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:179838200-179845800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:179838200-179846000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:179838200-179846200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:179841600-179846200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:179843800-179845800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:179843800-179846200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:179843800-179846200	Weak transcription	Lung	lung
11	chr1:179844000-179846200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:179844200-179845800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:179844200-179846000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:179844200-179846000	Weak transcription	Fetal Thymus	thymus
15	chr1:179844200-179846200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:179844400-179845800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr1:179844400-179846000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:179844400-179846200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:179844400-179846200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:179844400-179846200	Weak transcription	Left Ventricle	heart
21	chr1:179844400-179846200	Weak transcription	Pancreas	Pancrea
22	chr1:179844400-179846400	Weak transcription	Esophagus	oesophagus
23	chr1:179844400-179846400	Weak transcription	Gastric	stomach
24	chr1:179844600-179845800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:179844600-179846200	Enhancers	Colon Smooth Muscle	Colon
26	chr1:179844600-179847000	Active TSS	Placenta	Placenta
27	chr1:179844800-179845800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr1:179844800-179845800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr1:179844800-179845800	Flanking Active TSS	Osteobl	bone
30	chr1:179844800-179846000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:179844800-179846000	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr1:179844800-179846200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:179844800-179846200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr1:179844800-179846200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:179844800-179846200	Flanking Active TSS	HUVEC	blood vessel
36	chr1:179844800-179846600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:179844800-179847400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:179844800-179847400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:179845000-179845800	Enhancers	Primary hematopoietic stem cells	blood
40	chr1:179845000-179845800	Enhancers	Fetal Heart	heart
41	chr1:179845000-179846000	Enhancers	Primary T cells from cord blood	blood
42	chr1:179845000-179846200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:179845000-179846200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:179845000-179846200	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr1:179845000-179846200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:179845000-179846200	Transcr. at gene 5' and 3'	A549	lung
47	chr1:179845000-179846400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr1:179845000-179847200	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr1:179845000-179847200	Active TSS	Fetal Intestine Large	intestine
50	chr1:179845200-179845800	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links