Variant report

Variant	rs3843773
Chromosome Location	chr20:16265062-16265063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:16264271..16267069-chr20:16272916..16274482,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11087163	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12151916	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2031977	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2031978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2328012	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2328014	0.86[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6034443	0.99[ASN][1000 genomes]
rs6034445	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];0.99[ASN][1000 genomes]
rs6043847	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs6043851	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6043856	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6043857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6043859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6043862	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6043869	0.85[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs6043872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6075042	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6075043	0.95[CHB][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.96[ASN][1000 genomes]
rs6080201	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6080202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6080203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6080204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6080205	0.90[ASN][1000 genomes]
rs6080206	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs6080208	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs6080210	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6080211	0.91[CHB][hapmap]
rs6105563	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs6111011	0.81[ASN][1000 genomes]
rs73251232	0.92[ASN][1000 genomes]
rs928145	0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833930	chr20:16134347-16302763	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16242400-16275000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:16247600-16290800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr20:16248600-16291400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:16248800-16267000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr20:16248800-16272600	Weak transcription	Primary T cells from cord blood	blood
6	chr20:16249000-16272800	Weak transcription	Right Ventricle	heart
7	chr20:16249200-16277400	Weak transcription	Brain Substantia Nigra	brain
8	chr20:16250000-16266800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr20:16252000-16270800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr20:16252000-16289400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr20:16252400-16283000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr20:16253000-16277800	Weak transcription	Brain Angular Gyrus	brain
13	chr20:16253600-16268200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr20:16254000-16265200	Weak transcription	NHEK	skin
15	chr20:16254000-16278800	Weak transcription	Adipose Nuclei	Adipose
16	chr20:16254000-16281400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr20:16254000-16290800	Weak transcription	Esophagus	oesophagus
18	chr20:16254000-16298400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:16254200-16278600	Weak transcription	Pancreas	Pancrea
20	chr20:16254200-16284200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr20:16255400-16283000	Weak transcription	Fetal Lung	lung
22	chr20:16261400-16272800	Weak transcription	Osteobl	bone
23	chr20:16261600-16270800	Weak transcription	HepG2	liver
24	chr20:16262000-16266600	Weak transcription	Thymus	Thymus
25	chr20:16262600-16285400	Weak transcription	Ovary	ovary
26	chr20:16262600-16346200	Weak transcription	Gastric	stomach
27	chr20:16263000-16265600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr20:16263400-16265200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr20:16263600-16273200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:16263600-16277200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr20:16263800-16265600	Enhancers	Fetal Muscle Leg	muscle
32	chr20:16263800-16265800	Enhancers	Psoas Muscle	Psoas
33	chr20:16264200-16265600	Enhancers	Primary B cells from peripheral blood	blood
34	chr20:16264400-16265200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr20:16264400-16265200	Enhancers	Small Intestine	intestine
36	chr20:16264400-16265200	Enhancers	HSMM	muscle
37	chr20:16264400-16265600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr20:16264400-16265600	Enhancers	Fetal Intestine Large	intestine
39	chr20:16264400-16281600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr20:16264600-16265200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr20:16264600-16265400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr20:16264600-16265600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr20:16264600-16265600	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr20:16264600-16265600	Enhancers	Left Ventricle	heart
45	chr20:16264600-16284000	Weak transcription	Aorta	Aorta
46	chr20:16264800-16265200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr20:16264800-16265200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr20:16264800-16265400	Weak transcription	Fetal Intestine Small	intestine
49	chr20:16264800-16265400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr20:16264800-16290800	Weak transcription	Lung	lung

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