Variant report

Variant	rs1416823
Chromosome Location	chr1:180496582-180496583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180486527..180488396-chr1:180494744..180496710,2	MCF-7	breast:
2	chr1:180495119..180496658-chr1:180599630..180601968,2	K562	blood:
3	chr1:180495342..180496951-chr1:180619499..180622464,2	K562	blood:
4	chr1:180491722..180497520-chr1:180497939..180503107,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206905	Chromatin interaction
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10753211	0.81[CHB][hapmap]
rs10753216	0.82[ASN][1000 genomes]
rs10798759	0.81[CHB][hapmap]
rs10798762	0.81[CHB][hapmap]
rs10913969	0.90[CHB][hapmap]
rs10913980	0.81[CHB][hapmap]
rs10913981	0.81[CHB][hapmap]
rs10913984	0.81[CHB][hapmap]
rs10913985	0.81[CHB][hapmap]
rs10913994	0.90[CHB][hapmap]
rs10914018	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs11580793	0.81[CHB][hapmap]
rs12034217	0.81[CHB][hapmap]
rs12039331	0.84[ASN][1000 genomes]
rs12039933	0.90[CHB][hapmap]
rs12041620	1.00[ASN][1000 genomes]
rs12091722	0.90[CHB][hapmap]
rs12404209	0.90[CHB][hapmap]
rs12405902	0.90[CHB][hapmap]
rs12565492	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs12730889	0.81[CHB][hapmap]
rs1341924	0.90[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs1538620	0.81[CHB][hapmap]
rs16856086	1.00[ASN][1000 genomes]
rs16856087	0.96[ASN][1000 genomes]
rs1890731	0.85[ASN][1000 genomes]
rs2877415	0.90[CHB][hapmap]
rs3737584	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs3806300	0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs3806301	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs4076403	0.81[CHB][hapmap]
rs4421553	0.81[CHB][hapmap]
rs4543756	0.90[CHB][hapmap];0.83[CHD][hapmap]
rs4578179	0.80[CHB][hapmap]
rs4651064	0.81[CHB][hapmap]
rs4652505	0.80[CHB][hapmap]
rs6425634	0.90[CHB][hapmap]
rs6425644	0.94[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs6425645	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6670544	0.81[CHB][hapmap]
rs6699076	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704334	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs6704437	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs72720915	0.83[ASN][1000 genomes]
rs72720917	0.83[ASN][1000 genomes]
rs72720922	1.00[ASN][1000 genomes]
rs7528650	0.81[CHB][hapmap]
rs7532806	0.82[CHB][hapmap]
rs9701037	0.81[ASN][1000 genomes]
rs9726041	0.89[CHB][hapmap]
rs9730180	0.89[CHB][hapmap]

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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180486000-180499400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:180488000-180500400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:180488600-180497000	Enhancers	Placenta	Placenta
4	chr1:180491000-180499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:180491400-180499400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:180491600-180511200	Weak transcription	Psoas Muscle	Psoas
7	chr1:180492400-180499400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:180492400-180503000	Weak transcription	Pancreas	Pancrea
9	chr1:180492600-180498000	Weak transcription	HSMMtube	muscle
10	chr1:180493400-180496600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:180493800-180497000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:180494000-180496800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:180494000-180497200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:180494200-180502200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:180494200-180503000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:180494400-180508200	Weak transcription	Right Ventricle	heart
17	chr1:180494600-180497000	Enhancers	Fetal Intestine Small	intestine
18	chr1:180494600-180503000	Weak transcription	Fetal Lung	lung
19	chr1:180494800-180496600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:180494800-180497200	Enhancers	Fetal Intestine Large	intestine
21	chr1:180495000-180497000	Enhancers	Fetal Heart	heart
22	chr1:180495000-180497200	Enhancers	HMEC	breast
23	chr1:180495000-180499200	Weak transcription	Adipose Nuclei	Adipose
24	chr1:180495000-180499200	Weak transcription	Esophagus	oesophagus
25	chr1:180495000-180499200	Weak transcription	Lung	lung
26	chr1:180495000-180502200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:180495000-180503800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:180495200-180502600	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:180495400-180496800	Enhancers	HepG2	liver
30	chr1:180495400-180497000	Enhancers	K562	blood
31	chr1:180495600-180496800	Enhancers	Left Ventricle	heart
32	chr1:180495800-180496600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr1:180496000-180496600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:180496000-180496600	Enhancers	Right Atrium	heart
35	chr1:180496000-180496800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:180496000-180497000	Enhancers	HSMM	muscle
37	chr1:180496200-180496800	Enhancers	Hela-S3	cervix
38	chr1:180496200-180497000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:180496200-180497000	Enhancers	NH-A	brain
40	chr1:180496200-180497200	Enhancers	A549	lung
41	chr1:180496200-180497200	Enhancers	HUVEC	blood vessel
42	chr1:180496200-180498000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:180496400-180496600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr1:180496400-180496600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:180496400-180496800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:180496400-180496800	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr1:180496400-180497000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:180496400-180497000	Enhancers	NHEK	skin
49	chr1:180496400-180497000	Enhancers	Osteobl	bone
50	chr1:180496400-180497200	Enhancers	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links