Variant report

Variant	rs58642961
Chromosome Location	chr7:66144307-66144308
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr7:66144094-66144405	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:66143910-66144946	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr7:66144277-66146029	HepG2	liver:	n/a	n/a
4	MXI1	chr7:66143897-66144312	GM12878	blood:	n/a	n/a
5	POU2F2	chr7:66144003-66144373	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:66143751-66144317	SK-N-SH	brain:	n/a	n/a
7	POU2F2	chr7:66144028-66144317	GM12878	blood:	n/a	n/a
8	RUNX3	chr7:66143950-66144346	GM12878	blood:	n/a	n/a
9	POU2F2	chr7:66144007-66144370	GM12891	blood:	n/a	n/a
10	POU2F2	chr7:66144006-66144431	GM12891	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:66144088..66147004-chr7:66459962..66461648,2	MCF-7	breast:
2	chr7:66118403..66121534-chr7:66142637..66144652,3	K562	blood:
3	chr7:66134305..66137456-chr7:66140702..66144674,4	K562	blood:
4	chr7:66121223..66123141-chr7:66144196..66146928,3	MCF-7	breast:
5	chr7:66140247..66145111-chr7:66145587..66148696,5	K562	blood:
6	chr7:66118759..66121837-chr7:66141888..66144754,3	K562	blood:

No data

Variant related genes	Relation type
RABGEF1	TF binding region
ENSG00000126524	Chromatin interaction
ENSG00000226824	Chromatin interaction
ENSG00000198874	Chromatin interaction
ENSG00000154710	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11975957	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17138012	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17138015	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17138195	1.00[EUR][1000 genomes]
rs1882654	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58807488	1.00[EUR][1000 genomes]
rs60019603	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60319566	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6945895	1.00[EUR][1000 genomes]
rs6960788	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6964739	1.00[EUR][1000 genomes]
rs6964781	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6968492	0.87[AMR][1000 genomes]
rs7786451	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv981398	chr7:66138644-66147890	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66120600-66146000	Weak transcription	Primary T cells from cord blood	blood
2	chr7:66120600-66146200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:66120800-66146000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:66121000-66146200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:66121000-66146200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr7:66121400-66146000	Weak transcription	Adipose Nuclei	Adipose
7	chr7:66121400-66146000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:66121600-66145400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr7:66121600-66146200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr7:66121600-66146200	Weak transcription	HSMMtube	muscle
11	chr7:66122600-66146000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:66127800-66146000	Weak transcription	A549	lung
13	chr7:66128000-66145800	Weak transcription	Primary B cells from cord blood	blood
14	chr7:66128000-66146000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr7:66128000-66146000	Weak transcription	Fetal Lung	lung
16	chr7:66128000-66146000	Weak transcription	HSMM	muscle
17	chr7:66128000-66146200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:66128000-66146200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:66128000-66146400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:66131200-66146000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr7:66132400-66146000	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:66133600-66146000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:66134400-66146000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:66134400-66146400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr7:66134600-66145800	Weak transcription	Thymus	Thymus
26	chr7:66135000-66144800	Weak transcription	Dnd41	blood
27	chr7:66135000-66145800	Weak transcription	Placenta	Placenta
28	chr7:66135000-66146000	Weak transcription	Brain Germinal Matrix	brain
29	chr7:66135200-66144400	Weak transcription	Fetal Muscle Leg	muscle
30	chr7:66135200-66145800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr7:66135200-66146200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:66135200-66146200	Weak transcription	Fetal Brain Female	brain
33	chr7:66135200-66146200	Weak transcription	NHLF	lung
34	chr7:66135200-66146400	Weak transcription	Lung	lung
35	chr7:66135200-66146400	Weak transcription	Ovary	ovary
36	chr7:66135400-66145200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:66135400-66146000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr7:66135400-66146000	Weak transcription	HepG2	liver
39	chr7:66135400-66146400	Weak transcription	Esophagus	oesophagus
40	chr7:66135800-66146000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:66136200-66146200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:66136600-66146400	Weak transcription	Fetal Stomach	stomach
43	chr7:66137000-66144800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr7:66137000-66145800	Weak transcription	Brain Angular Gyrus	brain
45	chr7:66137000-66146000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:66137000-66146000	Weak transcription	Brain Hippocampus Middle	brain
47	chr7:66137000-66146200	Weak transcription	Right Ventricle	heart
48	chr7:66138400-66146000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr7:66138400-66146000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:66138400-66146000	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links