Variant report

Variant	rs56946978
Chromosome Location	chr1:165657080-165657081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165654992..165657269-chr1:165796152..165797744,2	MCF-7	breast:
2	chr1:165656454..165659398-chr1:165666338..165668915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143149	Chromatin interaction
ENSG00000215838	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000143183	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs16848958	1.00[EUR][1000 genomes]
rs16849238	1.00[EUR][1000 genomes]
rs16850696	1.00[AMR][1000 genomes]
rs16850707	1.00[AMR][1000 genomes]
rs2348731	1.00[EUR][1000 genomes]
rs2348836	1.00[AMR][1000 genomes]
rs57874110	1.00[AMR][1000 genomes]
rs58365780	1.00[EUR][1000 genomes]
rs58560842	1.00[AMR][1000 genomes]
rs60095346	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60308920	1.00[EUR][1000 genomes]
rs61125729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6658134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73014618	1.00[EUR][1000 genomes]
rs73014649	1.00[EUR][1000 genomes]
rs73027023	1.00[EUR][1000 genomes]
rs73027060	1.00[EUR][1000 genomes]
rs73028710	1.00[EUR][1000 genomes]
rs73029460	1.00[EUR][1000 genomes]
rs73029465	1.00[EUR][1000 genomes]
rs73029467	1.00[EUR][1000 genomes]
rs7528944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9333396	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165606200-165659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:165638000-165666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:165638600-165665400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:165639200-165659800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:165644800-165658800	Strong transcription	HSMM	muscle
6	chr1:165645000-165660200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:165645800-165657400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:165647800-165658400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:165650000-165666800	Weak transcription	Colonic Mucosa	Colon
10	chr1:165651600-165659600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:165651600-165665400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:165651600-165667200	Weak transcription	Gastric	stomach
13	chr1:165651800-165665200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:165651800-165665200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:165651800-165665400	Weak transcription	Small Intestine	intestine
16	chr1:165652000-165664000	Weak transcription	Fetal Brain Male	brain
17	chr1:165652200-165657400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:165652200-165665400	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:165652200-165665800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:165652200-165666000	Weak transcription	Fetal Kidney	kidney
21	chr1:165652200-165666800	Weak transcription	Lung	lung
22	chr1:165652400-165657200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:165652400-165657200	Weak transcription	HepG2	liver
24	chr1:165652400-165657400	Weak transcription	HUVEC	blood vessel
25	chr1:165652400-165658800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:165652400-165659200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:165652400-165659400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:165652400-165659600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:165652400-165659600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:165652400-165659600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:165652400-165659600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:165652400-165659800	Weak transcription	Brain Angular Gyrus	brain
33	chr1:165652400-165665200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:165652400-165665400	Weak transcription	HMEC	breast
35	chr1:165652400-165665400	Weak transcription	NH-A	brain
36	chr1:165652400-165665800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:165652400-165665800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:165652400-165665800	Weak transcription	HSMMtube	muscle
39	chr1:165652400-165666800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:165652400-165666800	Weak transcription	Esophagus	oesophagus
41	chr1:165652400-165667000	Weak transcription	Pancreas	Pancrea
42	chr1:165652400-165667000	Weak transcription	Spleen	Spleen
43	chr1:165652600-165657600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:165652600-165666000	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:165652800-165657400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:165652800-165657800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:165652800-165657800	Weak transcription	Ovary	ovary
48	chr1:165652800-165665400	Weak transcription	NHLF	lung
49	chr1:165652800-165666200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:165653000-165657400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links