Variant report

Variant	rs1551936
Chromosome Location	chr5:16545460-16545461
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16527956..16530319-chr5:16542721..16545847,3	K562	blood:
2	chr5:16465611..16467390-chr5:16543761..16546084,2	MCF-7	breast:
3	chr5:16463630..16466881-chr5:16544037..16546726,3	MCF-7	breast:
4	chr5:16544591..16547039-chr5:16547595..16549857,2	K562	blood:

Variant related genes	Relation type
ENSG00000173545	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10053236	0.92[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1020952	1.00[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.87[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12109050	0.92[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1240647	0.83[ASN][1000 genomes]
rs162758	0.87[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.94[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs162862	0.82[AFR][1000 genomes]
rs1991468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1991469	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1991470	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991471	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991472	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2019248	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2019260	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560831	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2560832	0.83[ASN][1000 genomes]
rs2617422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2617423	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2617424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2617425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2617426	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs31283	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs31288	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs334485	0.83[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs334486	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs334487	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs334490	0.82[ASN][1000 genomes]
rs334491	0.81[JPT][hapmap]
rs334492	0.81[ASN][1000 genomes]
rs425779	0.83[ASN][1000 genomes]
rs595358	0.82[ASN][1000 genomes]
rs6858960	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs899186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs991891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs994099	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881187	chr5:16514269-16654960	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr5:16522400-16567400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:16535600-16546000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:16536800-16552800	Weak transcription	Thymus	Thymus
4	chr5:16538600-16546400	Weak transcription	Right Ventricle	heart
5	chr5:16539200-16554400	Weak transcription	Small Intestine	intestine
6	chr5:16539800-16545600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:16539800-16545600	Weak transcription	Esophagus	oesophagus
8	chr5:16539800-16545800	Weak transcription	Pancreas	Pancrea
9	chr5:16539800-16546400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:16539800-16548400	Weak transcription	Aorta	Aorta
11	chr5:16539800-16548400	Weak transcription	Gastric	stomach
12	chr5:16541200-16547000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:16541200-16547000	Weak transcription	HSMM	muscle
14	chr5:16541200-16548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:16541200-16549600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:16541200-16552000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:16541400-16549800	Weak transcription	HMEC	breast
18	chr5:16542200-16547800	Enhancers	Brain Substantia Nigra	brain
19	chr5:16542600-16567200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:16543000-16545600	Weak transcription	Psoas Muscle	Psoas
21	chr5:16543200-16547200	Weak transcription	Fetal Intestine Large	intestine
22	chr5:16543200-16548400	Weak transcription	Primary T cells from cord blood	blood
23	chr5:16543200-16548400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:16543200-16591600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:16543400-16546800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:16543400-16547000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:16543400-16547200	Weak transcription	NH-A	brain
28	chr5:16543400-16552800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr5:16543600-16589800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:16544000-16562400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:16544200-16548800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr5:16544200-16549800	Enhancers	Brain Hippocampus Middle	brain
33	chr5:16544200-16550000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr5:16544200-16565200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:16544400-16549800	Enhancers	Fetal Heart	heart
36	chr5:16544400-16550200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr5:16544600-16549800	Enhancers	Brain Cingulate Gyrus	brain
38	chr5:16544600-16550000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:16544800-16545600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr5:16544800-16545600	Enhancers	NHDF-Ad	bronchial
41	chr5:16544800-16545800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:16544800-16546200	Enhancers	Brain Anterior Caudate	brain
43	chr5:16544800-16546200	Enhancers	NHEK	skin
44	chr5:16544800-16546400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:16545000-16546000	Enhancers	Placenta Amnion	Placenta Amnion
46	chr5:16545000-16546400	Enhancers	Brain Angular Gyrus	brain
47	chr5:16545000-16547000	Weak transcription	Fetal Intestine Small	intestine
48	chr5:16545000-16574600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr5:16545200-16545600	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr5:16545200-16545600	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links