Variant report

Variant	rs16945820
Chromosome Location	chr13:92008913-92008914
allele	A/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:75)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:75 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr13:92008144..92009724-chr20:42091800..42094586,2	K562	blood:
2	chr13:92007619..92012079-chr13:92329462..92332464,5	K562	blood:
3	chr13:92007639..92009819-chr13:92131676..92134611,2	K562	blood:
4	chr13:92007380..92009324-chr13:92011441..92013491,2	MCF-7	breast:
5	chr13:92008502..92010275-chr13:92333349..92335396,2	K562	blood:
6	chr13:92007131..92009056-chr9:134111257..134113529,2	K562	blood:
7	chr13:92006220..92010132-chr13:92106545..92110507,4	K562	blood:
8	chr13:91769596..91771444-chr13:92008291..92010121,2	K562	blood:
9	chr13:92008228..92010437-chr13:108592989..108595152,2	K562	blood:
10	chr13:92004766..92010130-chr13:92235897..92240121,6	K562	blood:
11	chr11:65273531..65275557-chr13:92007951..92010025,2	K562	blood:
12	chr13:92007765..92009366-chr13:92214136..92216197,2	K562	blood:
13	chr13:92006928..92009132-chr13:92273923..92276754,2	K562	blood:
14	chr13:92008413..92010506-chr13:92466310..92469194,2	K562	blood:
15	chr13:91920712..91923592-chr13:92007874..92010601,2	K562	blood:
16	chr13:91683791..91685341-chr13:92005987..92008919,2	K562	blood:
17	chr13:91893680..91897355-chr13:92007107..92011169,4	K562	blood:
18	chr11:27882899..27885879-chr13:92008840..92011260,2	K562	blood:
19	chr13:92008040..92009933-chr13:92191793..92193745,2	K562	blood:
20	chr13:92006517..92009365-chr9:134000918..134003856,2	K562	blood:
21	chr13:92006350..92012037-chr13:92182700..92187101,6	K562	blood:
22	chr13:92008103..92010063-chr9:133952155..133954983,2	K562	blood:
23	chr11:62608960..62610617-chr13:92006606..92010281,3	K562	blood:
24	chr13:92007566..92010436-chr13:108654648..108657460,2	K562	blood:
25	chr13:92008178..92010162-chr13:94344904..94347693,2	K562	blood:
26	chr13:92006840..92009442-chr13:92110730..92113341,2	K562	blood:
27	chr13:92007575..92011337-chr13:92428230..92431057,3	K562	blood:
28	chr13:91155632..91158016-chr13:92008294..92010443,2	K562	blood:
29	chr13:92007495..92010220-chr13:92160111..92163100,2	K562	blood:
30	chr13:91540464..91542436-chr13:92007500..92010085,2	K562	blood:
31	chr13:92008752..92010349-chr13:92203596..92205345,2	K562	blood:
32	chr13:92008212..92012126-chr13:92101857..92105185,4	K562	blood:
33	chr1:8928064..8929777-chr13:92008313..92011039,2	K562	blood:
34	chr13:92006709..92009565-chr19:18390813..18392345,2	K562	blood:
35	chr13:92008325..92009998-chr13:92343661..92346364,2	K562	blood:
36	chr13:91999461..92007353-chr13:92008154..92015149,15	MCF-7	breast:
37	chr13:91822541..91826333-chr13:92007078..92009162,4	K562	blood:
38	chr13:92008416..92011064-chr13:92130907..92133015,2	K562	blood:
39	chr13:91916595..91918707-chr13:92008662..92010951,3	K562	blood:
40	chr13:91851245..91855773-chr13:92007361..92011020,5	K562	blood:
41	chr13:91576022..91578508-chr13:92007800..92009778,2	K562	blood:
42	chr13:92007743..92009790-chr6:125854399..125855899,2	K562	blood:
43	chr13:92006631..92008993-chr13:92217984..92219908,2	K562	blood:
44	chr13:91808077..91809932-chr13:92006547..92009302,2	K562	blood:
45	chr13:91907666..91909561-chr13:92007500..92010207,2	K562	blood:
46	chr13:92008607..92010554-chr13:92155871..92158754,2	K562	blood:
47	chr13:92006945..92008960-chr13:92091324..92094208,2	K562	blood:
48	chr13:92006919..92009585-chr6:27098221..27101267,3	K562	blood:
49	chr13:92007364..92011025-chr13:92217645..92220635,3	K562	blood:
50	chr1:194758841..194760344-chr13:92007287..92009017,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215417	Chromatin interaction
ENSG00000145495	Chromatin interaction
ENSG00000259802	Chromatin interaction
ENSG00000050555	Chromatin interaction
ENSG00000126883	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000252622	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000130522	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12323299	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs16945806	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16945815	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28729540	1.00[AMR][1000 genomes]
rs3848048	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs7988366	1.00[AMR][1000 genomes]
rs9583916	1.00[AMR][1000 genomes]
rs9583917	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9589194	1.00[AMR][1000 genomes]
rs9589204	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9589205	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9589207	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9589208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9589216	1.00[AMR][1000 genomes]
rs9989081	0.87[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	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
5	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
6	nsv832679	chr13:91859467-92030220	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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	1943 gene(s)	inside rSNPs	diseases
7	esv1802171	chr13:91999737-92015977	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1940 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92001600-92010200	Weak transcription	Spleen	Spleen
2	chr13:92001600-92010800	Weak transcription	Pancreas	Pancrea
3	chr13:92001600-92012200	Weak transcription	Esophagus	oesophagus
4	chr13:92001800-92015600	Weak transcription	Ovary	ovary
5	chr13:92001800-92027200	Weak transcription	Aorta	Aorta
6	chr13:92002000-92011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr13:92002000-92011200	Weak transcription	Colonic Mucosa	Colon
8	chr13:92002000-92012200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr13:92002200-92010800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr13:92002400-92010800	Weak transcription	Brain Angular Gyrus	brain
11	chr13:92002400-92012000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr13:92002800-92009600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr13:92002800-92009800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr13:92002800-92010000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr13:92003000-92009000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr13:92003000-92009000	Weak transcription	Lung	lung
17	chr13:92003000-92009400	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr13:92003200-92010400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr13:92003400-92010000	Weak transcription	Fetal Brain Male	brain
20	chr13:92003400-92014000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr13:92003600-92009000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr13:92003600-92009200	Genic enhancers	Liver	Liver
23	chr13:92003600-92009200	Weak transcription	Brain Germinal Matrix	brain
24	chr13:92003600-92009600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:92003600-92010000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr13:92003600-92010000	Strong transcription	Fetal Muscle Leg	muscle
27	chr13:92003600-92010000	Strong transcription	NHEK	skin
28	chr13:92003600-92010800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr13:92003600-92010800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr13:92003600-92010800	Strong transcription	HSMM	muscle
31	chr13:92003600-92011800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr13:92003600-92012000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr13:92003600-92012600	Weak transcription	Brain Substantia Nigra	brain
34	chr13:92003600-92012800	Weak transcription	Small Intestine	intestine
35	chr13:92003600-92016600	Weak transcription	Gastric	stomach
36	chr13:92003600-92021200	Weak transcription	Right Ventricle	heart
37	chr13:92003600-92033200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:92003800-92010000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr13:92003800-92010600	Weak transcription	Psoas Muscle	Psoas
40	chr13:92003800-92010600	Weak transcription	Thymus	Thymus
41	chr13:92003800-92011000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr13:92003800-92011800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr13:92003800-92012200	Strong transcription	Fetal Thymus	thymus
44	chr13:92003800-92012200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr13:92003800-92012600	Weak transcription	Brain Hippocampus Middle	brain
46	chr13:92004000-92010800	Strong transcription	HUVEC	blood vessel
47	chr13:92004200-92010200	Strong transcription	NH-A	brain
48	chr13:92004400-92010400	Strong transcription	HMEC	breast
49	chr13:92004400-92010800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr13:92004600-92009800	Strong transcription	Muscle Satellite Cultured Cells	--

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