Variant report

Variant	rs2290998
Chromosome Location	chr19:38089458-38089459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38085211..38087419-chr19:38088303..38090305,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171817	Chromatin interaction
ENSG00000180479	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1016291	1.00[AFR][1000 genomes]
rs16958869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16972326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16973130	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16973541	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16973717	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16973886	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16973890	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16973919	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16974061	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16974358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16975375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16975696	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16975712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16975753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16975859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2045907	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2061779	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2306200	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2385128	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3795068	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3795070	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs41325249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4330033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4452074	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73632242	0.84[ASN][1000 genomes]
rs8107454	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8108032	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs955711	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38086400-38093400	Weak transcription	Gastric	stomach
2	chr19:38086400-38095600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr19:38086400-38095600	Weak transcription	Stomach Mucosa	stomach
4	chr19:38086600-38089600	Weak transcription	Pancreas	Pancrea
5	chr19:38086600-38089800	Weak transcription	Osteobl	bone
6	chr19:38086600-38090400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr19:38086600-38090800	Weak transcription	Psoas Muscle	Psoas
8	chr19:38086600-38091800	Weak transcription	Esophagus	oesophagus
9	chr19:38086600-38092000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:38086600-38092200	Weak transcription	Small Intestine	intestine
11	chr19:38086600-38092800	Weak transcription	Fetal Muscle Leg	muscle
12	chr19:38086600-38098200	Weak transcription	Colonic Mucosa	Colon
13	chr19:38086600-38098800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:38086600-38099400	Weak transcription	Fetal Stomach	stomach
15	chr19:38086600-38103200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:38086800-38090400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:38086800-38090400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:38086800-38090600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:38086800-38090800	Weak transcription	Fetal Intestine Large	intestine
20	chr19:38086800-38091800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:38086800-38092000	Weak transcription	Fetal Lung	lung
22	chr19:38086800-38094000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:38086800-38095600	Weak transcription	Fetal Kidney	kidney
24	chr19:38087200-38090400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:38087200-38090600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:38087200-38091800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:38087200-38093200	Weak transcription	Fetal Intestine Small	intestine
28	chr19:38087200-38099400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:38087200-38100200	Weak transcription	Right Ventricle	heart
30	chr19:38087200-38103000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr19:38087400-38090400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:38087400-38090400	Weak transcription	Dnd41	blood
33	chr19:38087400-38092000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:38087600-38091000	Weak transcription	Brain Germinal Matrix	brain
35	chr19:38087800-38094400	Weak transcription	Fetal Brain Male	brain
36	chr19:38087800-38107400	ZNF genes & repeats	Liver	Liver
37	chr19:38088000-38090800	Weak transcription	Fetal Brain Female	brain
38	chr19:38088400-38089600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:38088800-38090600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:38088800-38090600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr19:38088800-38092200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr19:38088800-38093800	ZNF genes & repeats	Ovary	ovary
43	chr19:38088800-38094000	Strong transcription	Primary T cells from cord blood	blood
44	chr19:38088800-38094000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr19:38088800-38094600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr19:38089000-38089600	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:38089000-38089800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:38089000-38090400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:38089000-38090600	Weak transcription	Primary B cells from cord blood	blood
50	chr19:38089000-38090800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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