Variant report

Variant	rs11879341
Chromosome Location	chr19:39631880-39631881
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	MXI1	chr19:39630332-39631882	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39625837..39627697-chr19:39631542..39633679,2	MCF-7	breast:
2	chr19:39616199..39617759-chr19:39631751..39634260,2	MCF-7	breast:
3	chr19:39622898..39624850-chr19:39631546..39633915,2	MCF-7	breast:
4	chr19:39630404..39632300-chr19:39634611..39637101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269172	TF binding region
ENSG00000269172	Chromatin interaction
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11878229	1.00[EUR][1000 genomes]
rs11878648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879084	1.00[YRI][hapmap];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]
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	0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16973231	1.00[CEU][hapmap];1.00[YRI][hapmap];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]
rs58909586	1.00[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]
rs7254479	1.00[MEX][hapmap]
rs7257753	1.00[MEX][hapmap]
rs7260015	1.00[CEU][hapmap];1.00[YRI][hapmap];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	0.83[YRI][hapmap];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	chr19:39628800-39632000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr19:39628800-39633600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:39629000-39632000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr19:39629000-39632000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:39629000-39632800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr19:39629000-39633600	Enhancers	Fetal Heart	heart
25	chr19:39629200-39632000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:39629200-39632000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr19:39629200-39633600	Enhancers	Ovary	ovary
28	chr19:39629200-39639400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:39629600-39632000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:39629600-39637600	Genic enhancers	Fetal Intestine Small	intestine
31	chr19:39629800-39632000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr19:39629800-39632800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:39630000-39633200	Enhancers	HepG2	liver
34	chr19:39630200-39633400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr19:39630200-39634800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:39630400-39635000	Weak transcription	NH-A	brain
37	chr19:39630600-39633200	Weak transcription	Colonic Mucosa	Colon
38	chr19:39630600-39634600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:39630600-39634800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:39630600-39635000	Weak transcription	Brain Angular Gyrus	brain
41	chr19:39630800-39632600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:39630800-39632800	Weak transcription	Lung	lung
43	chr19:39630800-39633200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr19:39630800-39635000	Weak transcription	Small Intestine	intestine
45	chr19:39630800-39646800	Weak transcription	Osteobl	bone
46	chr19:39630800-39651000	Weak transcription	NHDF-Ad	bronchial
47	chr19:39631000-39632400	Weak transcription	Stomach Mucosa	stomach
48	chr19:39631000-39632600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr19:39631000-39632600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:39631000-39632600	Weak transcription	Gastric	stomach

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