Variant report

Variant	rs58194712
Chromosome Location	chr20:1421416-1421417
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1413774..1421620-chr20:1445657..1450800,12	K562	blood:
2	chr20:1413566..1416812-chr20:1419779..1424298,4	K562	blood:
3	chr20:1419982..1421924-chr20:1432480..1435232,2	K562	blood:
4	chr20:1420415..1421693-chr20:1484065..1484901,6	MCF-7	breast:
5	chr20:1418037..1419774-chr20:1420141..1424100,3	MCF-7	breast:
6	chr20:1419111..1421909-chr20:1426787..1429297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11696447	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1474879	1.00[ASN][1000 genomes]
rs1474880	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2873522	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308086	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58718584	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59239479	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105101	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6105140	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109837	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109838	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109962	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109984	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109986	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109989	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109992	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66497853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124855	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs959813	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1405200-1422200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr20:1408200-1422600	Weak transcription	Fetal Brain Male	brain
3	chr20:1408600-1422400	Weak transcription	Colonic Mucosa	Colon
4	chr20:1408800-1422600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:1408800-1422600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:1408800-1423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:1410000-1422200	Weak transcription	Esophagus	oesophagus
8	chr20:1410200-1429000	Weak transcription	Stomach Mucosa	stomach
9	chr20:1411000-1422400	Weak transcription	Psoas Muscle	Psoas
10	chr20:1413200-1422600	Weak transcription	Fetal Kidney	kidney
11	chr20:1413800-1424200	Weak transcription	Colon Smooth Muscle	Colon
12	chr20:1415200-1422800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr20:1415400-1421800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr20:1415400-1422400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr20:1415400-1422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr20:1415600-1422600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr20:1415600-1423200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr20:1415800-1422000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr20:1416000-1421600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr20:1416000-1422000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr20:1416000-1422000	Weak transcription	HSMM	muscle
22	chr20:1416000-1422000	Weak transcription	NH-A	brain
23	chr20:1416000-1422200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr20:1416000-1422400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr20:1416000-1422400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr20:1416000-1422400	Weak transcription	Small Intestine	intestine
27	chr20:1416200-1421600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr20:1416200-1421800	Weak transcription	HMEC	breast
29	chr20:1416200-1422200	Weak transcription	HSMMtube	muscle
30	chr20:1416200-1422600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr20:1416200-1422600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr20:1416200-1422600	Weak transcription	NHEK	skin
33	chr20:1416200-1423200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr20:1416400-1421600	Weak transcription	Fetal Thymus	thymus
35	chr20:1416400-1422000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr20:1416400-1422400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr20:1416400-1422400	Weak transcription	GM12878-XiMat	blood
38	chr20:1416600-1422400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr20:1416800-1421600	Weak transcription	Dnd41	blood
40	chr20:1416800-1422200	Weak transcription	Osteobl	bone
41	chr20:1416800-1422600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr20:1416800-1422600	Weak transcription	NHDF-Ad	bronchial
43	chr20:1416800-1424200	Weak transcription	K562	blood
44	chr20:1417000-1422400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr20:1417000-1424600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr20:1417800-1422800	Weak transcription	HUVEC	blood vessel
47	chr20:1418400-1421800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr20:1418400-1422600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr20:1418400-1422800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr20:1418600-1425000	Weak transcription	Fetal Heart	heart

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