Variant report

Variant	rs2019099
Chromosome Location	chr2:190540716-190540717
allele	A/C
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	USF1	chr2:190540542-190540731	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190538834..190541562-chr2:190626367..190628350,2	MCF-7	breast:

Variant related genes	Relation type
ANKAR	TF binding region
ENSG00000253559	Chromatin interaction
ENSG00000128694	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1020151	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10209441	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10931429	1.00[ASW][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11888722	1.00[AMR][1000 genomes]
rs1225086	1.00[AMR][1000 genomes]
rs1225103	1.00[AMR][1000 genomes]
rs12693550	1.00[ASW][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs1437880	1.00[ASW][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1550241	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1550242	1.00[AMR][1000 genomes]
rs2118454	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2254040	0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs2263968	1.00[AMR][1000 genomes]
rs2352288	1.00[ASW][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs5742992	1.00[AMR][1000 genomes]
rs5742999	1.00[AMR][1000 genomes]
rs5743205	1.00[AMR][1000 genomes]
rs6723158	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs893782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs893783	0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs930426	1.00[ASW][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190528200-190541600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:190530000-190542800	Strong transcription	Dnd41	blood
3	chr2:190534000-190550200	Weak transcription	K562	blood
4	chr2:190539600-190543400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:190539800-190550200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:190539800-190550200	Weak transcription	Esophagus	oesophagus
7	chr2:190539800-190550200	Weak transcription	Small Intestine	intestine
8	chr2:190540000-190540800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:190540000-190540800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:190540000-190540800	Enhancers	Lung	lung
11	chr2:190540000-190540800	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr2:190540000-190542400	Weak transcription	Brain Germinal Matrix	brain
13	chr2:190540000-190542600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:190540000-190546000	Weak transcription	Gastric	stomach
15	chr2:190540000-190546000	Weak transcription	Left Ventricle	heart
16	chr2:190540000-190546000	Weak transcription	Ovary	ovary
17	chr2:190540000-190550200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:190540000-190550200	Weak transcription	Fetal Thymus	thymus
19	chr2:190540000-190550400	Weak transcription	Fetal Kidney	kidney
20	chr2:190540000-190563400	Weak transcription	Aorta	Aorta
21	chr2:190540200-190540800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:190540200-190540800	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:190540200-190540800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:190540200-190540800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr2:190540200-190540800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr2:190540200-190540800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:190540200-190540800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:190540200-190540800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr2:190540200-190540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:190540200-190540800	Enhancers	Liver	Liver
31	chr2:190540200-190540800	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr2:190540200-190540800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:190540200-190541000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr2:190540200-190541000	Weak transcription	Osteobl	bone
35	chr2:190540200-190541600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:190540200-190542400	Weak transcription	Fetal Intestine Large	intestine
37	chr2:190540200-190543000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr2:190540200-190543000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:190540200-190546600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:190540200-190547800	Weak transcription	HMEC	breast
41	chr2:190540200-190550200	Weak transcription	Right Atrium	heart
42	chr2:190540200-190550200	Weak transcription	Right Ventricle	heart
43	chr2:190540200-190578000	Weak transcription	Fetal Brain Male	brain
44	chr2:190540400-190540800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:190540400-190540800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:190540400-190540800	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:190540400-190540800	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr2:190540400-190540800	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr2:190540400-190540800	Enhancers	HepG2	liver
50	chr2:190540400-190541200	Weak transcription	A549	lung

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