Variant report

Variant	rs543054
Chromosome Location	chrX:154493106-154493107
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:
2	chrX:154444639..154446602-chrX:154492705..154495023,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224978	Chromatin interaction
ENSG00000155959	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11156600	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[MEX][hapmap]
rs11887	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap]
rs12013168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1393999	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3105275	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3105276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35296872	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs480210	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs4893113	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs492622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs496740	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs499428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs499669	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap]
rs504984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs507127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs516396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs519641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs520145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs523614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs524609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs525161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs533001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs542899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs544582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs547724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs559165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs568396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs573189	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap]
rs573572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs5940510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs5983697	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs5983764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6567813	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs782769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154490600-154493200	Weak transcription	HepG2	liver
2	chrX:154491400-154493200	Flanking Active TSS	Dnd41	blood
3	chrX:154491400-154494000	Active TSS	GM12878-XiMat	blood
4	chrX:154491400-154494200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chrX:154491400-154494200	Active TSS	Fetal Brain Female	brain
6	chrX:154491800-154494200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chrX:154491800-154494200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chrX:154491800-154494200	Active TSS	Brain Hippocampus Middle	brain
9	chrX:154492000-154493200	Active TSS	Brain Germinal Matrix	brain
10	chrX:154492000-154493200	Enhancers	Monocytes-CD14+_RO01746	blood
11	chrX:154492000-154494000	Active TSS	Brain Angular Gyrus	brain
12	chrX:154492000-154494000	Active TSS	Thymus	Thymus
13	chrX:154492000-154494200	Active TSS	Primary T cells fromperipheralblood	blood
14	chrX:154492000-154494200	Active TSS	Brain Cingulate Gyrus	brain
15	chrX:154492200-154493200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chrX:154492200-154494000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chrX:154492200-154494000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chrX:154492200-154494200	Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chrX:154492200-154494200	Active TSS	Brain Anterior Caudate	brain
20	chrX:154492400-154493200	Flanking Active TSS	Primary T cells from cord blood	blood
21	chrX:154492400-154493200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chrX:154492400-154493400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chrX:154492400-154494200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chrX:154492400-154494200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chrX:154492400-154494200	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chrX:154492400-154494200	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chrX:154492400-154494200	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chrX:154492600-154493200	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chrX:154492600-154493800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chrX:154492600-154493800	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chrX:154492600-154494000	Active TSS	H1 Cell Line	embryonic stem cell
32	chrX:154492600-154494000	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chrX:154492600-154494000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chrX:154492600-154494000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chrX:154492600-154494000	Active TSS	Brain Substantia Nigra	brain
36	chrX:154492600-154494000	Active TSS	Fetal Brain Male	brain
37	chrX:154492600-154494000	Active TSS	Fetal Thymus	thymus
38	chrX:154492600-154494200	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chrX:154492600-154494200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chrX:154492800-154493400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chrX:154492800-154493400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chrX:154492800-154493400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chrX:154492800-154493600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chrX:154492800-154493600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chrX:154492800-154493800	Active TSS	Duodenum Mucosa	Duodenum
46	chrX:154492800-154494000	Active TSS	H9 Cell Line	embryonic stem cell
47	chrX:154492800-154494000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chrX:154492800-154494000	Active TSS	Primary hematopoietic stem cells	blood
49	chrX:154492800-154494000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chrX:154492800-154494000	Active TSS	Fetal Kidney	kidney

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