Variant report

Variant	rs10408405
Chromosome Location	chr19:40929743-40929744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40919789..40935162-chr19:40946854..40955873,58	MCF-7	breast:
2	chr19:40852293..40855712-chr19:40925717..40929885,3	MCF-7	breast:
3	chr19:40929000..40933496-chr19:40948111..40953156,29	MCF-7	breast:
4	chr19:40929690..40933044-chr19:40967590..40972827,9	MCF-7	breast:
5	chr19:40929630..40934621-chr19:40969030..40973237,9	K562	blood:
6	chr19:40925645..40930180-chr19:40968953..40973278,5	MCF-7	breast:
7	chr19:40790880..40792731-chr19:40929438..40932853,4	K562	blood:
8	chr19:40925517..40930305-chr19:40937557..40941421,7	K562	blood:
9	chr19:40916047..40918713-chr19:40928638..40931104,2	MCF-7	breast:
10	chr19:40925098..40933993-chr19:40944045..40956524,41	K562	blood:
11	chr19:40924946..40933265-chr19:40969030..40973228,17	K562	blood:
12	chr19:40927385..40930245-chr19:41220973..41223399,2	MCF-7	breast:
13	chr19:40791054..40792631-chr19:40929438..40932083,2	K562	blood:
14	chr19:40928606..40931574-chr19:41013757..41016430,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105221	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000105223	Chromatin interaction
ENSG00000090013	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000160460	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10412156	1.00[EUR][1000 genomes]
rs10422945	1.00[EUR][1000 genomes]
rs10424704	1.00[EUR][1000 genomes]
rs11879375	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11881681	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13345497	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13346024	1.00[EUR][1000 genomes]
rs268659	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28407044	1.00[EUR][1000 genomes]
rs28679850	0.86[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	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55646097	0.94[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]
rs7256097	0.86[AFR][1000 genomes]
rs73559625	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73559626	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73559635	0.89[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	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
3	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
4	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
5	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
6	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
7	nsv911709	chr19:40928944-41060616	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40927400-40930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:40927600-40930400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:40927600-40930400	Weak transcription	Brain Substantia Nigra	brain
4	chr19:40927600-40930400	Weak transcription	Fetal Brain Female	brain
5	chr19:40927600-40930600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:40927600-40930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:40927600-40930600	Weak transcription	Brain Germinal Matrix	brain
8	chr19:40927800-40929800	Genic enhancers	Osteobl	bone
9	chr19:40927800-40930000	Weak transcription	Primary B cells from cord blood	blood
10	chr19:40927800-40930200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:40927800-40930200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:40927800-40930200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:40927800-40930400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:40927800-40930400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:40927800-40930400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:40927800-40930400	Enhancers	Rectal Smooth Muscle	rectum
17	chr19:40928000-40930000	Weak transcription	Small Intestine	intestine
18	chr19:40928000-40930400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:40928000-40930400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
20	chr19:40928200-40929800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
21	chr19:40928200-40930200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:40928400-40929800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:40928400-40929800	Genic enhancers	Adipose Nuclei	Adipose
24	chr19:40928400-40930000	Strong transcription	Fetal Intestine Small	intestine
25	chr19:40928400-40930200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:40928400-40930400	Weak transcription	Fetal Kidney	kidney
27	chr19:40928600-40930400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr19:40928800-40930000	Enhancers	Hela-S3	cervix
29	chr19:40928800-40930400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr19:40929000-40929800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr19:40929000-40930000	Weak transcription	Fetal Lung	lung
32	chr19:40929000-40930000	Enhancers	NH-A	brain
33	chr19:40929000-40930000	Weak transcription	NHEK	skin
34	chr19:40929000-40930400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:40929000-40930400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:40929000-40930400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr19:40929000-40930400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr19:40929000-40930400	Weak transcription	HepG2	liver
39	chr19:40929200-40929800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:40929200-40929800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr19:40929200-40930400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:40929200-40930400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr19:40929200-40930400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:40929200-40930400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr19:40929200-40930400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:40929200-40930400	Weak transcription	Brain Angular Gyrus	brain
47	chr19:40929200-40930400	Weak transcription	Brain Hippocampus Middle	brain
48	chr19:40929200-40930400	Weak transcription	Fetal Heart	heart
49	chr19:40929200-40930400	Weak transcription	Fetal Thymus	thymus
50	chr19:40929400-40929800	Weak transcription	Primary B cells from peripheral blood	blood

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