Variant report

Variant	rs6425644
Chromosome Location	chr1:180497834-180497835
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180497440..180500935-chr1:180506480..180510504,4	K562	blood:
2	chr1:180496778..180499562-chr1:180501152..180503837,3	K562	blood:
3	chr1:180470507..180472649-chr1:180497010..180499983,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135847	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10913994	0.86[JPT][hapmap]
rs10914007	0.83[JPT][hapmap]
rs10914023	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs12039331	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs12039933	0.86[JPT][hapmap]
rs12041620	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12136111	0.85[ASN][1000 genomes]
rs12404209	0.86[JPT][hapmap]
rs12405902	0.86[JPT][hapmap]
rs1341924	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1416823	0.94[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs1538622	0.81[CHB][hapmap]
rs16856086	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16856087	0.90[ASN][1000 genomes]
rs1890731	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1970400	0.88[EUR][1000 genomes]
rs2877415	0.86[JPT][hapmap]
rs3737584	0.81[CHB][hapmap]
rs3806300	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3806301	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4543756	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6425634	0.86[JPT][hapmap]
rs6425641	0.87[EUR][1000 genomes]
rs6425645	1.00[ASN][1000 genomes]
rs6687442	0.88[EUR][1000 genomes]
rs6687549	0.88[EUR][1000 genomes]
rs6699076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6699585	0.88[EUR][1000 genomes]
rs6704334	1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[EUR][1000 genomes]
rs6704437	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs72720915	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72720917	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72720922	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7513944	0.81[CHB][hapmap]
rs7521151	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7541993	0.88[CHB][hapmap]
rs7551178	0.81[CHB][hapmap]
rs7552084	0.87[CHB][hapmap]
rs946631	0.81[CHB][hapmap]
rs9701037	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9726041	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs9730180	1.00[CEU][hapmap];0.88[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	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:46 , 50 per page) page: 1

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	chr1:180491000-180499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:180491400-180499400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:180491600-180511200	Weak transcription	Psoas Muscle	Psoas
6	chr1:180492400-180499400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:180492400-180503000	Weak transcription	Pancreas	Pancrea
8	chr1:180492600-180498000	Weak transcription	HSMMtube	muscle
9	chr1:180494200-180502200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:180494200-180503000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:180494400-180508200	Weak transcription	Right Ventricle	heart
12	chr1:180494600-180503000	Weak transcription	Fetal Lung	lung
13	chr1:180495000-180499200	Weak transcription	Adipose Nuclei	Adipose
14	chr1:180495000-180499200	Weak transcription	Esophagus	oesophagus
15	chr1:180495000-180499200	Weak transcription	Lung	lung
16	chr1:180495000-180502200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:180495000-180503800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:180495200-180502600	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:180496200-180498000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:180496400-180499400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:180496600-180499200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:180496600-180499400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:180496600-180499600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:180496600-180508000	Weak transcription	Right Atrium	heart
25	chr1:180496800-180499200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:180496800-180499200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:180496800-180499200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:180496800-180499200	Weak transcription	Hela-S3	cervix
29	chr1:180496800-180499200	Weak transcription	HepG2	liver
30	chr1:180496800-180503600	Weak transcription	Left Ventricle	heart
31	chr1:180497000-180498200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:180497000-180499200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:180497000-180499200	Weak transcription	Fetal Intestine Small	intestine
34	chr1:180497000-180499200	Weak transcription	Placenta	Placenta
35	chr1:180497000-180499200	Weak transcription	HSMM	muscle
36	chr1:180497000-180499200	Weak transcription	NH-A	brain
37	chr1:180497000-180499200	Weak transcription	NHEK	skin
38	chr1:180497000-180499400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:180497000-180499400	Weak transcription	Osteobl	bone
40	chr1:180497000-180502400	Weak transcription	Fetal Heart	heart
41	chr1:180497000-180502600	Weak transcription	K562	blood
42	chr1:180497200-180498200	Weak transcription	HMEC	breast
43	chr1:180497200-180499200	Weak transcription	A549	lung
44	chr1:180497600-180500200	Enhancers	HUVEC	blood vessel
45	chr1:180497800-180498200	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr1:180497800-180511200	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links