Variant report

Variant	rs6437620
Chromosome Location	chr3:105552878-105552879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:105552724..105554590-chr3:105555325..105557862,2	K562	blood:
2	chr3:105552676..105554224-chr3:105555679..105557862,2	K562	blood:
3	chr3:105546357..105547931-chr3:105552831..105554477,2	K562	blood:
4	chr3:105533973..105536078-chr3:105552694..105554794,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1021858	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1021859	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1039544	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10511246	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1075739	0.81[ASN][1000 genomes]
rs11921710	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11924742	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12633654	0.84[ASN][1000 genomes]
rs12633854	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12635232	0.81[ASN][1000 genomes]
rs12637560	0.89[ASN][1000 genomes]
rs12637809	0.82[ASN][1000 genomes]
rs12639271	0.81[ASN][1000 genomes]
rs1503921	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1561922	0.85[ASN][1000 genomes]
rs16851523	0.81[ASN][1000 genomes]
rs16851539	0.81[ASN][1000 genomes]
rs16851563	0.83[ASN][1000 genomes]
rs16851570	0.83[ASN][1000 genomes]
rs16851587	0.81[ASN][1000 genomes]
rs16851630	0.89[ASN][1000 genomes]
rs1867192	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910499	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1947000	0.83[ASN][1000 genomes]
rs2089091	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197208	0.82[ASN][1000 genomes]
rs2197209	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894840	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57520912	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58340800	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59534462	0.89[ASN][1000 genomes]
rs59611997	0.84[ASN][1000 genomes]
rs60619938	0.82[ASN][1000 genomes]
rs6437621	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437626	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6767627	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6804152	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73854891	0.85[ASN][1000 genomes]
rs73854894	0.89[ASN][1000 genomes]
rs73857222	0.88[ASN][1000 genomes]
rs7619449	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7624400	0.82[ASN][1000 genomes]
rs7629357	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634844	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7641825	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7648842	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649466	0.83[EUR][1000 genomes]
rs9631436	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9657904	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9789988	0.82[ASN][1000 genomes]
rs9826886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846534	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869648	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9874600	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv508234	chr3:105549864-105565806	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
2	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
3	chr3:105528400-105553600	Weak transcription	Fetal Kidney	kidney
4	chr3:105532200-105563000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:105533600-105560600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:105533800-105570000	Weak transcription	Dnd41	blood
7	chr3:105534200-105566200	Weak transcription	Brain Germinal Matrix	brain
8	chr3:105535600-105553800	Weak transcription	Fetal Brain Male	brain
9	chr3:105540800-105569600	Weak transcription	Fetal Thymus	thymus
10	chr3:105541000-105554400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:105541800-105553600	Weak transcription	Fetal Brain Female	brain
12	chr3:105542200-105553600	Weak transcription	Liver	Liver
13	chr3:105542200-105554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:105542600-105555400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:105542600-105566000	Weak transcription	Fetal Stomach	stomach
16	chr3:105542800-105554400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:105543000-105555600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:105543400-105555800	Weak transcription	HepG2	liver
19	chr3:105543400-105560800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:105543400-105581200	Weak transcription	Gastric	stomach
21	chr3:105543600-105557200	Weak transcription	Fetal Intestine Large	intestine
22	chr3:105543800-105571000	Weak transcription	Lung	lung
23	chr3:105544000-105554400	Weak transcription	Fetal Lung	lung
24	chr3:105544200-105554400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:105544200-105559200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:105544200-105584600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:105545400-105553000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
29	chr3:105546800-105553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:105546800-105560800	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:105547200-105553600	Weak transcription	Hela-S3	cervix
32	chr3:105547200-105554600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:105547200-105554800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:105547200-105554800	Weak transcription	Ovary	ovary
35	chr3:105547200-105555000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:105547200-105557400	Weak transcription	Fetal Intestine Small	intestine
37	chr3:105547400-105554400	Weak transcription	NH-A	brain
38	chr3:105547400-105557200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:105547800-105554600	Weak transcription	HMEC	breast
40	chr3:105547800-105554800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:105547800-105555400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:105547800-105557400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:105548200-105553600	Weak transcription	A549	lung
44	chr3:105548200-105553800	Weak transcription	NHLF	lung
45	chr3:105548400-105561200	Weak transcription	K562	blood
46	chr3:105548400-105561400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:105548600-105559600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:105549000-105553800	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:105549000-105554600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:105549000-105555000	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links