Variant report

Variant	rs249040
Chromosome Location	chr5:79751332-79751333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79738646..79740760-chr5:79750273..79752228,2	K562	blood:

Variant related genes	Relation type
ENSG00000039319	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1097309	0.81[AFR][1000 genomes]
rs1363775	0.93[AFR][1000 genomes]
rs168939	0.80[AFR][1000 genomes]
rs174075	0.93[AFR][1000 genomes]
rs185100	0.97[AFR][1000 genomes]
rs187479	0.89[AFR][1000 genomes]
rs194540	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249015	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs249018	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs249019	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs249020	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs249021	0.93[AFR][1000 genomes]
rs249024	0.93[AFR][1000 genomes]
rs249025	0.91[AFR][1000 genomes]
rs249026	0.93[AFR][1000 genomes]
rs249027	0.93[AFR][1000 genomes]
rs249028	0.93[AFR][1000 genomes]
rs249029	0.93[AFR][1000 genomes]
rs249031	0.93[AFR][1000 genomes]
rs249033	0.85[AFR][1000 genomes]
rs249039	0.96[AFR][1000 genomes]
rs2544599	0.82[AFR][1000 genomes]
rs2544600	0.82[AFR][1000 genomes]
rs2544603	0.94[AFR][1000 genomes]
rs259032	0.86[AFR][1000 genomes]
rs259033	0.93[AFR][1000 genomes]
rs259034	0.94[AFR][1000 genomes]
rs3095850	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3095851	0.81[AFR][1000 genomes]
rs3096112	0.80[EUR][1000 genomes]
rs401612	0.93[AFR][1000 genomes]
rs969567	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer 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	49 gene(s)	inside rSNPs	diseases
2	nsv1028027	chr5:79694699-79841752	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79704600-79758000	Weak transcription	Spleen	Spleen
2	chr5:79704600-79758600	Weak transcription	Gastric	stomach
3	chr5:79705600-79757400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:79722600-79765400	Weak transcription	Fetal Brain Male	brain
5	chr5:79724200-79757400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:79729800-79752800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:79730000-79756400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:79730000-79757000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:79730200-79751800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr5:79730200-79761400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:79730200-79762200	Weak transcription	Stomach Mucosa	stomach
12	chr5:79730600-79757200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:79730600-79762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:79731400-79768000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:79731600-79758400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:79732200-79757400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:79732200-79757800	Weak transcription	NHEK	skin
18	chr5:79732200-79758600	Weak transcription	Esophagus	oesophagus
19	chr5:79732200-79766200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:79732400-79758200	Weak transcription	Small Intestine	intestine
21	chr5:79733400-79782600	Weak transcription	NHLF	lung
22	chr5:79733600-79757200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:79733800-79755000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr5:79735000-79751800	Weak transcription	Brain Angular Gyrus	brain
25	chr5:79735000-79758600	Weak transcription	K562	blood
26	chr5:79736400-79757400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:79736400-79759600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:79737000-79752600	Weak transcription	Psoas Muscle	Psoas
29	chr5:79737200-79752200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:79738000-79761800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:79738800-79758600	Strong transcription	Liver	Liver
32	chr5:79739200-79756000	Weak transcription	Fetal Heart	heart
33	chr5:79739600-79757200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:79739800-79752600	Weak transcription	Fetal Thymus	thymus
35	chr5:79739800-79757400	Weak transcription	Lung	lung
36	chr5:79739800-79758000	Weak transcription	Thymus	Thymus
37	chr5:79739800-79760000	Weak transcription	Right Ventricle	heart
38	chr5:79740800-79752200	Weak transcription	Fetal Kidney	kidney
39	chr5:79741000-79752600	Weak transcription	Brain Germinal Matrix	brain
40	chr5:79741400-79752400	Weak transcription	HMEC	breast
41	chr5:79741600-79755200	Weak transcription	Colon Smooth Muscle	Colon
42	chr5:79741600-79757200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:79743000-79752600	Weak transcription	NH-A	brain
44	chr5:79743000-79757400	Weak transcription	Fetal Intestine Small	intestine
45	chr5:79743600-79752600	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:79743600-79752600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:79743600-79757400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:79743600-79757400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr5:79743600-79757400	Weak transcription	Aorta	Aorta
50	chr5:79743800-79757400	Weak transcription	Fetal Brain Female	brain

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