Variant report

Variant	rs547776
Chromosome Location	chr1:179870919-179870920
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179845449..179848601-chr1:179867688..179872232,4	K562	blood:
2	chr1:179850058..179853356-chr1:179869131..179876291,8	K562	blood:
3	chr1:179849896..179853295-chr1:179868800..179873439,8	K562	blood:

Variant related genes	Relation type
ENSG00000169905	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1144575	0.95[ASN][1000 genomes]
rs1148812	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1148815	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12062341	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062383	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281378	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281408	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1281411	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1281412	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1281413	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281428	0.93[ASN][1000 genomes]
rs1281429	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281430	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281432	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1298477	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1298479	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1300068	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007148	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245425	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249346	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2762858	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777908	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777909	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2777917	0.90[AMR][1000 genomes]
rs2794582	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2794583	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs474258	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475233	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475434	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479094	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480377	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480498	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486906	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs501300	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs505789	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs505837	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507603	0.92[ASN][1000 genomes]
rs514421	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs518774	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522534	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530369	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs530854	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs531814	0.81[EUR][1000 genomes]
rs538512	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549650	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553830	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555270	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555526	0.93[ASN][1000 genomes]
rs589780	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs599185	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600046	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600553	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605807	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609521	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612215	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs644412	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6657364	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179852800-179871200	Weak transcription	Spleen	Spleen
2	chr1:179853000-179884800	Weak transcription	Esophagus	oesophagus
3	chr1:179853000-179890400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:179853200-179886600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:179853200-179890800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:179853400-179872600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:179853400-179877000	Weak transcription	Right Ventricle	heart
8	chr1:179853400-179878200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:179853400-179882800	Weak transcription	Fetal Brain Male	brain
10	chr1:179854000-179886800	Weak transcription	Fetal Heart	heart
11	chr1:179854200-179871800	Weak transcription	Brain Germinal Matrix	brain
12	chr1:179855600-179871600	Weak transcription	A549	lung
13	chr1:179856200-179876800	Weak transcription	NHLF	lung
14	chr1:179857600-179871600	Weak transcription	HSMM	muscle
15	chr1:179857600-179886800	Weak transcription	Psoas Muscle	Psoas
16	chr1:179860000-179873800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:179860200-179890200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:179860400-179871600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:179860400-179873000	Weak transcription	HUVEC	blood vessel
20	chr1:179860400-179873200	Weak transcription	K562	blood
21	chr1:179860400-179878800	Weak transcription	Colonic Mucosa	Colon
22	chr1:179860600-179871600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:179861000-179871400	Weak transcription	NHEK	skin
24	chr1:179861000-179871600	Weak transcription	Brain Substantia Nigra	brain
25	chr1:179861200-179871400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:179861200-179878000	Weak transcription	Gastric	stomach
27	chr1:179861200-179886600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:179861400-179871000	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:179861400-179871600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:179861400-179871600	Weak transcription	Aorta	Aorta
31	chr1:179861400-179871600	Weak transcription	HSMMtube	muscle
32	chr1:179861400-179882200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:179861600-179871400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:179861600-179871600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:179861600-179871600	Weak transcription	Thymus	Thymus
36	chr1:179861600-179871600	Weak transcription	HepG2	liver
37	chr1:179861600-179872600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:179861600-179872600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:179861600-179886600	Weak transcription	Pancreas	Pancrea
40	chr1:179863000-179871200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:179863000-179871200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:179863000-179871600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:179863000-179871600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:179863000-179871600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:179863000-179876800	Weak transcription	Fetal Kidney	kidney
46	chr1:179863200-179871400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:179863200-179871600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:179863200-179877400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:179864000-179871600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:179864000-179871800	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links