Variant report

Variant	rs55910561
Chromosome Location	chr13:52321754-52321755
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1058141	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1058142	0.91[AFR][1000 genomes]
rs1060562	0.90[AFR][1000 genomes]
rs10676	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12427805	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12428478	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430600	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430760	0.88[AMR][1000 genomes]
rs17069413	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs17075849	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs2011276	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2296027	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2408491	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4399447	0.81[AMR][1000 genomes]
rs57280031	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57837262	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59291282	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199739	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199742	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73199750	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7321346	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs7329391	0.95[AMR][1000 genomes]
rs74086223	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs7985214	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001480	0.88[AMR][1000 genomes]
rs9526795	0.87[AFR][1000 genomes]
rs9535754	0.85[AFR][1000 genomes]
rs9568662	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9596572	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9596573	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer 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	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
6	nsv455887	chr13:52318522-52405251	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv561645	chr13:52318522-52405251	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52288400-52322200	Weak transcription	K562	blood
2	chr13:52296400-52322200	Weak transcription	Fetal Heart	heart
3	chr13:52298000-52322200	Weak transcription	Fetal Brain Female	brain
4	chr13:52300400-52322200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr13:52300600-52321800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr13:52305000-52338200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr13:52305400-52321800	Weak transcription	Gastric	stomach
8	chr13:52305800-52322000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:52306000-52322200	Weak transcription	Left Ventricle	heart
10	chr13:52306000-52322200	Weak transcription	Right Ventricle	heart
11	chr13:52306200-52339000	Weak transcription	Fetal Kidney	kidney
12	chr13:52308000-52322200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:52308200-52322200	Weak transcription	Stomach Mucosa	stomach
14	chr13:52308200-52342800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr13:52308400-52326800	Weak transcription	Hela-S3	cervix
16	chr13:52309800-52322200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr13:52310000-52321800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr13:52312600-52322200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr13:52314000-52321800	Strong transcription	HSMM	muscle
20	chr13:52314000-52322600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr13:52314200-52322200	Weak transcription	A549	lung
22	chr13:52314200-52326600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr13:52314400-52322000	Weak transcription	NHLF	lung
24	chr13:52314600-52321800	Weak transcription	Esophagus	oesophagus
25	chr13:52314600-52322200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr13:52315000-52322000	Weak transcription	Fetal Intestine Large	intestine
27	chr13:52315200-52322000	Weak transcription	NHDF-Ad	bronchial
28	chr13:52315200-52327000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr13:52315400-52321800	Weak transcription	Fetal Lung	lung
30	chr13:52315400-52322400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr13:52315600-52328600	Weak transcription	Brain Germinal Matrix	brain
32	chr13:52315600-52332200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:52315800-52321800	Weak transcription	Placenta	Placenta
34	chr13:52315800-52321800	Weak transcription	Thymus	Thymus
35	chr13:52316000-52321800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr13:52316200-52321800	Weak transcription	Fetal Muscle Leg	muscle
37	chr13:52316200-52322200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr13:52316200-52322200	Weak transcription	Colon Smooth Muscle	Colon
39	chr13:52316200-52322200	Weak transcription	Fetal Stomach	stomach
40	chr13:52316200-52322200	Weak transcription	Fetal Thymus	thymus
41	chr13:52316200-52332200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr13:52316400-52321800	Weak transcription	Lung	lung
43	chr13:52316400-52322000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr13:52316400-52322200	Weak transcription	Spleen	Spleen
45	chr13:52316400-52329400	Weak transcription	Brain Anterior Caudate	brain
46	chr13:52317200-52321800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr13:52317400-52321800	Weak transcription	Adipose Nuclei	Adipose
48	chr13:52317600-52322200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr13:52318400-52322000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr13:52318400-52334200	Weak transcription	Fetal Brain Male	brain

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