Variant report

Variant	rs6658767
Chromosome Location	chr1:94529895-94529896
allele	C/T
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	RAD21	chr1:94528376-94530003	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:94529516-94530145	SK-N-SH	brain:	n/a	n/a
3	GATA2	chr1:94529696-94529961	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94528533..94530442-chr1:94567755..94569846,3	MCF-7	breast:
2	chr1:94529817..94533865-chr1:94534670..94536843,3	MCF-7	breast:

Variant related genes	Relation type
ABCA4	TF binding region

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17392507	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1801581	1.00[AFR][1000 genomes]
rs41292683	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4147835	0.87[EUR][1000 genomes]
rs55712710	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56197337	0.87[EUR][1000 genomes]
rs56375042	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72725166	0.83[AMR][1000 genomes]
rs72725167	0.87[EUR][1000 genomes]
rs72725169	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72725178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72725182	1.00[AMR][1000 genomes];1.00[EUR][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	nsv871172	chr1:94504545-94535546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv871057	chr1:94513142-94577286	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94521000-94534400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:94522200-94533800	Weak transcription	Aorta	Aorta
3	chr1:94522600-94533200	Weak transcription	Gastric	stomach
4	chr1:94522800-94533400	Weak transcription	Stomach Mucosa	stomach
5	chr1:94523200-94533600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:94523600-94530400	Enhancers	Left Ventricle	heart
7	chr1:94524600-94531200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:94525000-94530600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:94526000-94530200	Enhancers	HUVEC	blood vessel
10	chr1:94526000-94530400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:94526200-94533600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:94526600-94530200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:94526800-94530200	Enhancers	NHDF-Ad	bronchial
14	chr1:94527000-94530200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:94527000-94531200	Enhancers	Placenta	Placenta
16	chr1:94527200-94530000	Enhancers	Fetal Heart	heart
17	chr1:94527200-94530000	Enhancers	NHLF	lung
18	chr1:94527400-94530000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:94527600-94532200	Weak transcription	Thymus	Thymus
20	chr1:94527600-94534200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:94527800-94530200	Enhancers	HepG2	liver
22	chr1:94527800-94534400	Weak transcription	HSMMtube	muscle
23	chr1:94528000-94533000	Weak transcription	HMEC	breast
24	chr1:94528000-94533200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:94528000-94533800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:94528000-94534400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:94528200-94533000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:94528600-94530000	Enhancers	Colon Smooth Muscle	Colon
29	chr1:94528600-94530000	Enhancers	Fetal Lung	lung
30	chr1:94528600-94530200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:94528600-94530200	Enhancers	Ovary	ovary
32	chr1:94528600-94530400	Enhancers	Adipose Nuclei	Adipose
33	chr1:94528800-94530000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
34	chr1:94528800-94530000	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr1:94528800-94530200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr1:94528800-94530600	Enhancers	Fetal Kidney	kidney
37	chr1:94528800-94530600	Enhancers	Fetal Stomach	stomach
38	chr1:94529000-94533600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:94529000-94533600	Weak transcription	HSMM	muscle
40	chr1:94529200-94530000	Enhancers	Psoas Muscle	Psoas
41	chr1:94529200-94530000	Enhancers	Small Intestine	intestine
42	chr1:94529200-94533600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:94529400-94532000	Weak transcription	Fetal Thymus	thymus
44	chr1:94529400-94532200	Weak transcription	NH-A	brain
45	chr1:94529400-94533000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:94529400-94533600	Weak transcription	Fetal Intestine Large	intestine
47	chr1:94529400-94533800	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:94529600-94530000	Enhancers	Right Atrium	heart
49	chr1:94529600-94530200	Enhancers	Fetal Muscle Trunk	muscle
50	chr1:94529600-94531600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links