Variant report

Variant	rs518879
Chromosome Location	chr6:149659648-149659649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149649733..149652455-chr6:149658613..149661110,2	K562	blood:
2	chr6:149654628..149657508-chr6:149659280..149661788,2	MCF-7	breast:
3	chr6:149652416..149655199-chr6:149659324..149661368,2	K562	blood:
4	chr6:149658537..149661655-chr6:149675884..149678661,3	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs17086451	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2341783	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341784	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744427	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744428	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744431	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2744433	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2744434	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2789487	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2789489	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2789490	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789500	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734296	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4360154	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs472620	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs472810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474369	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478531	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs478767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480526	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480778	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs481769	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897117	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs490529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs492956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504762	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511105	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs513923	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs515133	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs532008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532250	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs533026	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538386	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554926	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556335	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564405	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs565825	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs570442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588028	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60006373	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs600739	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630642	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs641068	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs652514	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs652921	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs663625	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674919	0.80[EUR][1000 genomes]
rs681919	0.84[EUR][1000 genomes]
rs92605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373591	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9377216	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9377217	0.80[EUR][1000 genomes]
rs9390676	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399686	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9404032	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9404034	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404035	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9404037	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149641200-149681400	Weak transcription	Fetal Stomach	stomach
2	chr6:149641600-149660200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr6:149641800-149660200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:149645000-149666400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:149648400-149660600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:149649000-149660200	Weak transcription	Fetal Intestine Small	intestine
7	chr6:149649400-149689400	Weak transcription	Fetal Brain Female	brain
8	chr6:149649800-149660200	Weak transcription	Gastric	stomach
9	chr6:149651400-149660000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:149651400-149660000	Enhancers	Liver	Liver
11	chr6:149652600-149659800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:149652800-149660000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:149653200-149660200	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:149654000-149674200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:149654600-149668600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:149655400-149660200	Enhancers	Stomach Mucosa	stomach
17	chr6:149655600-149659800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr6:149655800-149659800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:149655800-149659800	Enhancers	Primary B cells from cord blood	blood
20	chr6:149655800-149660200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:149656200-149670800	Weak transcription	Esophagus	oesophagus
22	chr6:149656800-149660000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:149656800-149660200	Enhancers	Brain Angular Gyrus	brain
24	chr6:149656800-149661800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:149656800-149681400	Weak transcription	Psoas Muscle	Psoas
26	chr6:149656800-149682400	Weak transcription	Lung	lung
27	chr6:149656800-149694400	Weak transcription	Placenta	Placenta
28	chr6:149657000-149660200	Enhancers	Brain Hippocampus Middle	brain
29	chr6:149657000-149660400	Enhancers	Fetal Heart	heart
30	chr6:149657400-149660000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:149657400-149663600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:149657400-149665800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:149657600-149660200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr6:149657600-149663200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:149657800-149659800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr6:149657800-149660000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr6:149657800-149661400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:149657800-149673800	Weak transcription	Thymus	Thymus
39	chr6:149657800-149683800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:149657800-149691200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:149658000-149660000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:149658000-149661200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:149658000-149661400	Weak transcription	HSMM	muscle
44	chr6:149658000-149662800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr6:149658000-149663200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:149658000-149663200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr6:149658000-149663400	Weak transcription	Small Intestine	intestine
48	chr6:149658000-149663800	Weak transcription	Aorta	Aorta
49	chr6:149658000-149663800	Weak transcription	Right Ventricle	heart
50	chr6:149658000-149673800	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links