Variant report

Variant	rs62278057
Chromosome Location	chr3:160943054-160943055
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	GATA3	chr3:160941970-160943186	MCF-7	breast:	n/a	chr3:160943048-160943061
2	POLR2A	chr3:160941329-160943182	MCF-7	breast:	n/a	n/a
3	POLR2A	chr3:160942672-160943061	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160942925..160944989-chr3:161039772..161043116,3	MCF-7	breast:
2	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
3	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
4	chr3:160819564..160821281-chr3:160942870..160944755,2	MCF-7	breast:
5	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271052	TF binding region
ENSG00000169255	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16832137	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62278054	0.81[EUR][1000 genomes]
rs62278056	0.82[EUR][1000 genomes]
rs62279886	0.84[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160940000-160971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:160940000-160977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:160940200-160943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:160940200-160965400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:160940800-160946600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:160940800-160946600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:160940800-160956000	Weak transcription	Colonic Mucosa	Colon
9	chr3:160941000-160943400	Active TSS	GM12878-XiMat	blood
10	chr3:160941000-160943800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:160941000-160946400	Weak transcription	Brain Substantia Nigra	brain
12	chr3:160941000-160946400	Weak transcription	Lung	lung
13	chr3:160941000-160946400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:160941000-160946600	Weak transcription	Thymus	Thymus
15	chr3:160941000-160956000	Weak transcription	Esophagus	oesophagus
16	chr3:160941000-160969600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:160941000-160970200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:160941000-160974800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:160941000-160983000	Weak transcription	Spleen	Spleen
20	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
21	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
22	chr3:160941200-160943400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:160941200-160943800	Weak transcription	Aorta	Aorta
24	chr3:160941200-160944800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:160941200-160945800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:160941200-160946000	Weak transcription	HSMMtube	muscle
27	chr3:160941200-160946400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:160941200-160946800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:160941200-160968600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:160941200-160969800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:160941200-160973400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:160941400-160943200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:160941400-160943200	Genic enhancers	Hela-S3	cervix
34	chr3:160941400-160943800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:160941400-160971800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:160941600-160943600	Genic enhancers	Dnd41	blood
37	chr3:160941600-160944600	Weak transcription	NHLF	lung
38	chr3:160941600-160944800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:160941600-160946400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:160941600-160946400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:160941600-160969800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:160941600-160975400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:160941800-160943600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:160941800-160944400	Weak transcription	A549	lung
45	chr3:160941800-160945200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:160941800-160946400	Weak transcription	Psoas Muscle	Psoas
47	chr3:160941800-160947200	Weak transcription	Fetal Brain Female	brain
48	chr3:160941800-160948000	Weak transcription	Brain Germinal Matrix	brain
49	chr3:160941800-160948200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:160941800-160948600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links