Variant report

Variant	rs58909586
Chromosome Location	chr19:39631348-39631349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr19:39631167-39631356	HepG2	liver:	n/a	n/a
2	ZNF263	chr19:39630976-39631462	HEK293-T-REx	kidney:	n/a	n/a
3	MXI1	chr19:39630332-39631882	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr19:39630559-39631614	K562	blood:	n/a	n/a
5	EP300	chr19:39629606-39631875	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr19:39631300-39631450	HRPEpiC	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39628877..39631480-chr19:39652977..39654703,2	K562	blood:
2	chr19:39628513..39631605-chr19:39651561..39654703,3	K562	blood:
3	chr19:39622591..39626006-chr19:39627126..39631368,3	MCF-7	breast:
4	chr19:39630404..39632300-chr19:39634611..39637101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269172	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11878229	1.00[EUR][1000 genomes]
rs11878648	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879084	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879196	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880984	1.00[EUR][1000 genomes]
rs11881029	1.00[EUR][1000 genomes]
rs11882129	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882668	1.00[EUR][1000 genomes]
rs11882711	1.00[EUR][1000 genomes]
rs11882955	1.00[EUR][1000 genomes]
rs16973211	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16973231	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57716250	1.00[EUR][1000 genomes]
rs57769351	1.00[EUR][1000 genomes]
rs58626126	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59303188	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60229944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61641657	1.00[EUR][1000 genomes]
rs7246294	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7254424	1.00[EUR][1000 genomes]
rs7260015	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73549583	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549585	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73549593	1.00[AMR][1000 genomes]
rs73549600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73551720	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73551786	1.00[EUR][1000 genomes]
rs73553708	1.00[EUR][1000 genomes]
rs73553711	1.00[EUR][1000 genomes]
rs73553738	1.00[EUR][1000 genomes]
rs73553740	1.00[EUR][1000 genomes]
rs73553742	1.00[EUR][1000 genomes]
rs73930290	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73930300	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73933809	1.00[EUR][1000 genomes]
rs73933837	1.00[EUR][1000 genomes]
rs8101586	1.00[EUR][1000 genomes]
rs8111473	1.00[EUR][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	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617000-39635000	Weak transcription	Aorta	Aorta
2	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
4	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr19:39622400-39635200	Weak transcription	Fetal Brain Female	brain
6	chr19:39622600-39639600	Weak transcription	HSMM	muscle
7	chr19:39623000-39635200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:39624000-39647000	Weak transcription	NHLF	lung
10	chr19:39624200-39634800	Weak transcription	Fetal Kidney	kidney
11	chr19:39624800-39632600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:39624800-39633000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr19:39627200-39646800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:39627400-39632000	Enhancers	Brain Germinal Matrix	brain
15	chr19:39627600-39634400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:39627600-39635000	Weak transcription	NHEK	skin
17	chr19:39627600-39641200	Weak transcription	Hela-S3	cervix
18	chr19:39627600-39645800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr19:39628600-39631800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:39628800-39631600	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr19:39628800-39631800	Genic enhancers	A549	lung
22	chr19:39628800-39632000	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr19:39628800-39633600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:39629000-39631400	Enhancers	Fetal Muscle Leg	muscle
25	chr19:39629000-39631600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:39629000-39631600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:39629000-39631800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:39629000-39631800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr19:39629000-39631800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr19:39629000-39631800	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr19:39629000-39631800	Enhancers	Placenta	Placenta
32	chr19:39629000-39631800	Enhancers	Right Ventricle	heart
33	chr19:39629000-39632000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr19:39629000-39632000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:39629000-39632800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr19:39629000-39633600	Enhancers	Fetal Heart	heart
37	chr19:39629200-39631400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:39629200-39631400	Enhancers	Brain Anterior Caudate	brain
39	chr19:39629200-39631600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:39629200-39632000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:39629200-39632000	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr19:39629200-39633600	Enhancers	Ovary	ovary
43	chr19:39629200-39639400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:39629400-39631400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:39629400-39631400	Enhancers	Colon Smooth Muscle	Colon
46	chr19:39629400-39631600	Genic enhancers	Fetal Stomach	stomach
47	chr19:39629400-39631800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr19:39629400-39631800	Enhancers	Fetal Intestine Large	intestine
49	chr19:39629600-39631400	Enhancers	Placenta Amnion	Placenta Amnion
50	chr19:39629600-39632000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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