Variant report

Variant	rs11879375
Chromosome Location	chr19:40914027-40914028
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40907794..40914181-chr19:40946949..40951155,9	K562	blood:
2	chr19:40913782..40916099-chr19:40948894..40950431,2	MCF-7	breast:
3	chr19:40913411..40914921-chr19:40919245..40922077,2	MCF-7	breast:
4	chr19:40912468..40914220-chr19:40946700..40948513,2	K562	blood:
5	chr19:40911341..40916843-chr19:40917541..40922029,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105227	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000167565	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10408405	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10412156	1.00[EUR][1000 genomes]
rs10422945	1.00[EUR][1000 genomes]
rs10424704	1.00[EUR][1000 genomes]
rs11881681	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13345497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13346024	1.00[EUR][1000 genomes]
rs268659	1.00[EUR][1000 genomes]
rs28407044	1.00[EUR][1000 genomes]
rs28679850	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28728269	1.00[EUR][1000 genomes]
rs3730257	1.00[EUR][1000 genomes]
rs4150984	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55646097	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55860305	1.00[EUR][1000 genomes]
rs55954198	1.00[EUR][1000 genomes]
rs59129285	1.00[EUR][1000 genomes]
rs60115762	1.00[EUR][1000 genomes]
rs61018633	1.00[EUR][1000 genomes]
rs73559625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73559626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73559635	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73933256	1.00[EUR][1000 genomes]
rs73933258	1.00[EUR][1000 genomes]
rs73933265	1.00[EUR][1000 genomes]
rs73933270	1.00[EUR][1000 genomes]
rs73933276	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
7	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40910200-40916800	Weak transcription	Right Atrium	heart
2	chr19:40910200-40917000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr19:40910200-40917000	Weak transcription	Esophagus	oesophagus
4	chr19:40910200-40917000	Weak transcription	Psoas Muscle	Psoas
5	chr19:40910200-40919000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:40910200-40926800	Weak transcription	Gastric	stomach
7	chr19:40910600-40915600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:40910600-40915600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:40910600-40915800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:40910600-40916800	Weak transcription	Fetal Heart	heart
11	chr19:40910600-40917000	Weak transcription	Fetal Intestine Small	intestine
12	chr19:40910600-40917000	Weak transcription	NHEK	skin
13	chr19:40910600-40918400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:40910600-40921000	Weak transcription	Fetal Kidney	kidney
15	chr19:40910600-40922800	Weak transcription	Fetal Thymus	thymus
16	chr19:40910800-40914200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:40910800-40915800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:40911000-40917000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr19:40911200-40915800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:40911200-40917000	Weak transcription	Placenta	Placenta
21	chr19:40911400-40915600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr19:40911400-40915600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:40911400-40915600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr19:40911400-40915800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:40911400-40915800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr19:40911400-40915800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:40911400-40916800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr19:40913400-40914400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:40913600-40914200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr19:40913600-40914400	Enhancers	Primary B cells from cord blood	blood
31	chr19:40913600-40914400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr19:40913600-40914400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:40913600-40914400	Genic enhancers	Lung	lung
34	chr19:40913600-40914600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr19:40913600-40914600	Enhancers	Primary B cells from peripheral blood	blood
36	chr19:40913600-40914600	Enhancers	Primary hematopoietic stem cells	blood
37	chr19:40913600-40914800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr19:40913600-40914800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr19:40913600-40915000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:40913600-40915200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:40913800-40914200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr19:40913800-40914200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr19:40913800-40914200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:40913800-40914200	Enhancers	Left Ventricle	heart
45	chr19:40913800-40914200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr19:40913800-40914400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:40913800-40914400	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr19:40913800-40914400	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr19:40913800-40914400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:40913800-40914400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links