Variant report

Variant	rs4889170
Chromosome Location	chr16:80655406-80655407
allele	A/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	chr16:80654063..80656286-chr16:80664938..80666580,2	MCF-7	breast:
2	chr16:80655167..80656068-chr16:80871542..80872135,2	MCF-7	breast:
3	chr16:80654095..80656173-chr16:80667578..80669313,2	MCF-7	breast:
4	chr16:80559928..80561785-chr16:80653051..80655923,2	MCF-7	breast:
5	chr16:80654459..80656206-chr16:80752582..80754185,2	MCF-7	breast:
6	chr16:80653224..80655610-chr16:80835327..80837663,2	MCF-7	breast:
7	chr16:80653589..80657400-chr16:80657593..80661612,3	K562	blood:
8	chr16:80654014..80661253-chr16:80836600..80840694,9	MCF-7	breast:
9	chr16:80654804..80656514-chr16:80661613..80663917,2	MCF-7	breast:
10	chr16:80653017..80657135-chr16:80751314..80754331,4	MCF-7	breast:
11	chr16:79071364..79071874-chr16:80655306..80655850,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166446	Chromatin interaction
ENSG00000260064	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1109546	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12448290	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs13329877	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2123279	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2123280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2123281	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4325579	0.87[AMR][1000 genomes]
rs4586445	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4888100	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4888101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4888102	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4888103	0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4889166	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4889167	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889169	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4889171	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4889172	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4889173	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4889174	0.83[AFR][1000 genomes]
rs4889176	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4889177	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4889178	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4889179	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4889180	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4889181	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56713233	0.81[EUR][1000 genomes]
rs57872556	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59946023	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60236050	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60992426	0.83[EUR][1000 genomes]
rs74028350	0.83[EUR][1000 genomes]
rs74028368	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8057859	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs8059592	1.00[CEU][hapmap]
rs9924170	0.99[EUR][1000 genomes]
rs9927571	0.95[JPT][hapmap]

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	nsv1060621	chr16:80532848-80980616	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv542989	chr16:80532848-80980616	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1056083	chr16:80636184-80666779	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1063971	chr16:80640278-80663092	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1063761	chr16:80640278-80663665	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1055196	chr16:80647550-80672417	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1057562	chr16:80650768-80675842	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80630600-80668000	Weak transcription	Fetal Kidney	kidney
2	chr16:80634200-80663600	Weak transcription	Brain Anterior Caudate	brain
3	chr16:80635400-80655600	Weak transcription	Brain Angular Gyrus	brain
4	chr16:80639800-80657400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr16:80640600-80662200	Weak transcription	Primary T cells from cord blood	blood
6	chr16:80640600-80662600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr16:80640800-80663800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr16:80640800-80669200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr16:80642200-80668200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr16:80642800-80663800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr16:80644200-80666200	Weak transcription	Brain Substantia Nigra	brain
12	chr16:80645400-80657600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:80646000-80656000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr16:80646400-80657800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr16:80646400-80662200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr16:80646400-80662200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr16:80646600-80657800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr16:80646600-80687800	Weak transcription	Pancreas	Pancrea
19	chr16:80647000-80665000	Weak transcription	Gastric	stomach
20	chr16:80649600-80657800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr16:80649600-80658000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr16:80650000-80661800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr16:80650400-80659800	Strong transcription	Hela-S3	cervix
24	chr16:80650800-80656200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr16:80652800-80657000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr16:80653000-80655800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr16:80653200-80668200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr16:80653600-80657600	Weak transcription	Lung	lung
29	chr16:80653600-80658400	Enhancers	Placenta	Placenta
30	chr16:80653600-80662200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr16:80653600-80666800	Weak transcription	Esophagus	oesophagus
32	chr16:80653600-80667400	Weak transcription	Fetal Stomach	stomach
33	chr16:80653800-80657800	Weak transcription	Adipose Nuclei	Adipose
34	chr16:80653800-80662000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr16:80654000-80655600	Enhancers	Placenta Amnion	Placenta Amnion
36	chr16:80654000-80657800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr16:80654200-80656200	Weak transcription	Fetal Intestine Large	intestine
38	chr16:80654200-80657000	Weak transcription	HUVEC	blood vessel
39	chr16:80654200-80657600	Weak transcription	HSMMtube	muscle
40	chr16:80654200-80658400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr16:80654400-80657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr16:80654400-80657200	Weak transcription	Spleen	Spleen
43	chr16:80654400-80657200	Weak transcription	NHEK	skin
44	chr16:80654400-80657600	Weak transcription	Aorta	Aorta
45	chr16:80654400-80662000	Weak transcription	Liver	Liver
46	chr16:80654400-80667800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr16:80654400-80668800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr16:80654600-80657800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr16:80654800-80657200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr16:80654800-80662200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links