Variant report

Variant	rs5983697
Chromosome Location	chrX:154492424-154492425
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:154440871..154443205-chrX:154491979..154493717,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224978	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11156600	0.91[CHB][hapmap]
rs11887	1.00[CHB][hapmap]
rs12013168	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs1393999	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs3105275	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3105276	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs35296872	1.00[CHB][hapmap]
rs480210	0.91[CHB][hapmap]
rs4893113	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs492622	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs496740	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs499428	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs499669	1.00[CHB][hapmap]
rs504984	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs507127	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs516396	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs519641	0.90[CHB][hapmap]
rs520145	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs523614	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs524609	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs525161	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs533001	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs542899	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs543054	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs544582	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs547724	0.91[CHB][hapmap]
rs559165	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs568396	0.91[CHB][hapmap]
rs573189	0.91[CHB][hapmap]
rs573572	0.90[CHB][hapmap]
rs5940510	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs5983764	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs5987090	0.83[CHB][hapmap]
rs6567813	1.00[CHB][hapmap]
rs782769	0.91[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916671	chrX:154418093-154560374	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv532966	chrX:154418093-154721378	Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv29972	chrX:154418093-154929412	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv532965	chrX:154418093-155226096	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv532967	chrX:154418093-155252027	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534387	chrX:154455491-154560375	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154485400-154493000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chrX:154487000-154492600	Weak transcription	Fetal Thymus	thymus
3	chrX:154487200-154492600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chrX:154489400-154492800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chrX:154490400-154493000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chrX:154490600-154492800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chrX:154490600-154493200	Weak transcription	HepG2	liver
8	chrX:154491200-154492800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chrX:154491400-154492600	Enhancers	Fetal Brain Male	brain
10	chrX:154491400-154493200	Flanking Active TSS	Dnd41	blood
11	chrX:154491400-154494000	Active TSS	GM12878-XiMat	blood
12	chrX:154491400-154494200	Active TSS	Brain Inferior Temporal Lobe	brain
13	chrX:154491400-154494200	Active TSS	Fetal Brain Female	brain
14	chrX:154491600-154492600	Enhancers	Primary B cells from peripheral blood	blood
15	chrX:154491800-154494200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chrX:154491800-154494200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chrX:154491800-154494200	Active TSS	Brain Hippocampus Middle	brain
18	chrX:154492000-154492800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chrX:154492000-154492800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chrX:154492000-154493200	Active TSS	Brain Germinal Matrix	brain
21	chrX:154492000-154493200	Enhancers	Monocytes-CD14+_RO01746	blood
22	chrX:154492000-154494000	Active TSS	Brain Angular Gyrus	brain
23	chrX:154492000-154494000	Active TSS	Thymus	Thymus
24	chrX:154492000-154494200	Active TSS	Primary T cells fromperipheralblood	blood
25	chrX:154492000-154494200	Active TSS	Brain Cingulate Gyrus	brain
26	chrX:154492200-154492600	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chrX:154492200-154492600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chrX:154492200-154492600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chrX:154492200-154493200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chrX:154492200-154494000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chrX:154492200-154494000	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chrX:154492200-154494200	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chrX:154492200-154494200	Active TSS	Brain Anterior Caudate	brain
34	chrX:154492400-154492600	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chrX:154492400-154492600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chrX:154492400-154492600	Enhancers	Brain Substantia Nigra	brain
37	chrX:154492400-154492600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chrX:154492400-154492800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chrX:154492400-154492800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chrX:154492400-154493000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chrX:154492400-154493200	Flanking Active TSS	Primary T cells from cord blood	blood
42	chrX:154492400-154493200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chrX:154492400-154493400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chrX:154492400-154494200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chrX:154492400-154494200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chrX:154492400-154494200	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chrX:154492400-154494200	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chrX:154492400-154494200	Active TSS	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links