Variant report

Variant	rs59710738
Chromosome Location	chr6:80579937-80579938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NRF1	chr6:80579357-80579945	GM12878	blood:	n/a	n/a
2	CTCF	chr6:80579078-80580081	A549	lung:	n/a	chr6:80579479-80579497 chr6:80579480-80579496 chr6:80579474-80579495 chr6:80579481-80579494
3	RAD21	chr6:80577105-80580479	SK-N-SH	brain:	n/a	chr6:80578023-80578042 chr6:80579004-80579018 chr6:80579461-80579475 chr6:80579484-80579498 chr6:80578027-80578037 chr6:80579477-80579496
4	SMC3	chr6:80578768-80580026	SK-N-SH	brain:	n/a	chr6:80579481-80579495

No.	Distal block	Cell Line	Cell type
1	chr6:80577959..80580872-chr6:80588146..80590140,2	K562	blood:
2	chr6:80488189..80489092-chr6:80579221..80580068,2	K562	blood:
3	chr6:80579385..80581106-chr6:80583521..80585496,2	K562	blood:

Variant related genes	Relation type
ENSG00000233835	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10806180	0.89[ASN][1000 genomes]
rs12196014	0.89[ASN][1000 genomes]
rs163768	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs163973	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs343682	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs346283	0.94[ASN][1000 genomes]
rs346288	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs346297	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs346307	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs346314	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1021143	chr6:80400195-80598163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	esv3693359	chr6:80539454-80606537	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80576600-80582200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:80577400-80583400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:80577600-80580000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr6:80577600-80583200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:80577800-80580000	Enhancers	Fetal Heart	heart
6	chr6:80577800-80580200	Enhancers	HMEC	breast
7	chr6:80578000-80580000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:80578000-80582800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:80579000-80580000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:80579000-80580000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr6:80579000-80580000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr6:80579000-80580000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr6:80579000-80580000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr6:80579000-80580000	Enhancers	Fetal Thymus	thymus
15	chr6:80579000-80580200	Enhancers	NHEK	skin
16	chr6:80579200-80580000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:80579200-80580000	Enhancers	Primary B cells from peripheral blood	blood
18	chr6:80579200-80580000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:80579200-80580000	Enhancers	Fetal Intestine Small	intestine
20	chr6:80579200-80580000	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr6:80579200-80580400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:80579400-80580000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
23	chr6:80579400-80580000	Active TSS	Primary hematopoietic stem cells	blood
24	chr6:80579400-80580000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:80579400-80580000	Flanking Active TSS	Dnd41	blood
26	chr6:80579600-80580000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr6:80579600-80580000	Flanking Active TSS	Liver	Liver
28	chr6:80579600-80580000	Enhancers	Colon Smooth Muscle	Colon
29	chr6:80579600-80580000	Enhancers	Duodenum Mucosa	Duodenum
30	chr6:80579600-80580000	Active TSS	GM12878-XiMat	blood
31	chr6:80579600-80580000	Flanking Active TSS	Hela-S3	cervix
32	chr6:80579600-80580000	Enhancers	K562	blood
33	chr6:80579600-80580000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr6:80579800-80580000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:80579800-80580000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr6:80579800-80580000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:80579800-80580000	Enhancers	Brain Angular Gyrus	brain
38	chr6:80579800-80580000	Enhancers	Brain Anterior Caudate	brain
39	chr6:80579800-80580000	Enhancers	Brain Cingulate Gyrus	brain
40	chr6:80579800-80580000	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr6:80579800-80580000	Enhancers	Thymus	Thymus
42	chr6:80579800-80580000	Flanking Bivalent TSS/Enh	HepG2	liver
43	chr6:80579800-80580000	Enhancers	HUVEC	blood vessel
44	chr6:80579800-80580200	Enhancers	Primary T cells from cord blood	blood
45	chr6:80579800-80580800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:80579800-80580800	Weak transcription	Stomach Mucosa	stomach
47	chr6:80579800-80581000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr6:80579800-80581200	Enhancers	Brain Germinal Matrix	brain
49	chr6:80579800-80582200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:80579800-80582600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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