Variant report

Variant	rs10417715
Chromosome Location	chr19:19427576-19427577
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19421328..19423836-chr19:19425744..19428285,2	K562	blood:
2	chr19:19383714..19386060-chr19:19425012..19427870,3	K562	blood:
3	chr19:19417598..19419748-chr19:19425185..19428061,2	MCF-7	breast:
4	chr19:19424971..19429019-chr19:19429642..19432591,7	K562	blood:
5	chr19:19301690..19304194-chr19:19425927..19428019,2	MCF-7	breast:
6	chr19:19413265..19416143-chr19:19426604..19429701,3	K562	blood:

Variant related genes	Relation type
ENSG00000129933	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000213996	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000267629	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000064490	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10402799	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403737	0.94[YRI][hapmap]
rs10405475	0.92[YRI][hapmap]
rs10408216	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10413309	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416335	1.00[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs10417312	0.89[AMR][1000 genomes]
rs10422331	0.86[AFR][1000 genomes]
rs10422522	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10422620	0.86[AFR][1000 genomes]
rs10423535	0.94[YRI][hapmap]
rs10423747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425084	1.00[MKK][hapmap]
rs11879483	1.00[CHD][hapmap]
rs12327663	1.00[AFR][1000 genomes]
rs16996031	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes]
rs16996042	0.89[ASW][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16996102	0.94[YRI][hapmap]
rs2106699	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2315280	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28437425	0.96[AFR][1000 genomes]
rs28857503	0.96[AFR][1000 genomes]
rs55877107	0.90[AFR][1000 genomes]
rs56304704	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56317107	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60860168	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7248765	1.00[AMR][1000 genomes]
rs7249940	1.00[AMR][1000 genomes]
rs73922864	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922870	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8110508	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19384400-19430600	Weak transcription	Right Atrium	heart
2	chr19:19385400-19428400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:19386800-19428400	Strong transcription	Fetal Intestine Small	intestine
4	chr19:19388000-19429000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:19390800-19430000	Weak transcription	Psoas Muscle	Psoas
6	chr19:19402400-19427600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:19402400-19427800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr19:19402800-19427600	Strong transcription	Fetal Intestine Large	intestine
9	chr19:19402800-19428600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:19403000-19427800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr19:19403400-19427800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:19403400-19428600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr19:19403800-19428200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr19:19404000-19427600	Strong transcription	Fetal Muscle Leg	muscle
15	chr19:19404200-19429000	Strong transcription	Fetal Stomach	stomach
16	chr19:19404600-19427600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr19:19404600-19427600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:19404800-19428600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:19405000-19427800	Strong transcription	Thymus	Thymus
20	chr19:19407000-19428200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:19408200-19428400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:19410800-19428400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr19:19410800-19428600	Strong transcription	Fetal Thymus	thymus
24	chr19:19411000-19427800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr19:19411000-19428200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr19:19411200-19427600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:19411200-19427600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:19411200-19427600	Strong transcription	Primary T cells from cord blood	blood
29	chr19:19411200-19427600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:19411200-19427600	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:19411200-19427800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr19:19411200-19427800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:19411200-19427800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:19411200-19427800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:19411200-19428200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr19:19411200-19428200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr19:19411200-19428400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:19411200-19428400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:19411600-19427600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr19:19411600-19427600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:19411800-19427600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr19:19416000-19427600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr19:19416000-19427800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:19416200-19427600	Strong transcription	Brain Angular Gyrus	brain
45	chr19:19416200-19428000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr19:19416200-19430000	Weak transcription	Fetal Brain Male	brain
47	chr19:19416800-19427800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:19419400-19427800	Strong transcription	Spleen	Spleen
49	chr19:19419400-19429400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr19:19419600-19429600	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links