Variant report

Variant	rs573572
Chromosome Location	chrX:154494178-154494179
allele	C/T
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	MXI1	chrX:154493176-154494217	SK-N-SH	brain:	n/a	n/a
2	MAFK	chrX:154493197-154494260	GM12878	blood:	n/a	chrX:154493796-154493806 chrX:154493797-154493806
3	SIN3AK20	chrX:154493235-154494201	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:154444639..154446602-chrX:154492705..154495023,2	MCF-7	breast:

Variant related genes	Relation type
RAB39B	TF binding region
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];0.89[MEX][hapmap]
rs11887	0.85[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs12013168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap]
rs1393999	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap]
rs3105275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap]
rs3105276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap]
rs35296872	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[TSI][hapmap]
rs480210	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs4893113	1.00[CHB][hapmap]
rs492622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap]
rs496740	1.00[CHB][hapmap]
rs499428	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap]
rs499669	0.91[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap]
rs504984	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap]
rs507127	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap]
rs516396	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap]
rs519641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs520145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap]
rs523614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap]
rs524609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap]
rs525161	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap]
rs533001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap]
rs542899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap]
rs543054	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]
rs544582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap]
rs547724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap]
rs559165	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap]
rs568396	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap]
rs573189	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[MEX][hapmap]
rs5940510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap]
rs5983697	0.90[CHB][hapmap]
rs5983764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap]
rs6567813	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs782769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154491400-154494200	Active TSS	Brain Inferior Temporal Lobe	brain
2	chrX:154491400-154494200	Active TSS	Fetal Brain Female	brain
3	chrX:154491800-154494200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chrX:154491800-154494200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chrX:154491800-154494200	Active TSS	Brain Hippocampus Middle	brain
6	chrX:154492000-154494200	Active TSS	Primary T cells fromperipheralblood	blood
7	chrX:154492000-154494200	Active TSS	Brain Cingulate Gyrus	brain
8	chrX:154492200-154494200	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chrX:154492200-154494200	Active TSS	Brain Anterior Caudate	brain
10	chrX:154492400-154494200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chrX:154492400-154494200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chrX:154492400-154494200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chrX:154492400-154494200	Active TSS	Primary T helper cells PMA-I stimulated	--
14	chrX:154492400-154494200	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chrX:154492600-154494200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chrX:154492600-154494200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chrX:154492800-154494200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chrX:154493000-154494200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chrX:154493000-154494200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chrX:154493000-154494200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chrX:154493000-154494200	Active TSS	Primary B cells from cord blood	blood
22	chrX:154493000-154494200	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chrX:154493200-154494200	Active TSS	Primary B cells from peripheral blood	blood
24	chrX:154493400-154494200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chrX:154493400-154494200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chrX:154493400-154494200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chrX:154493400-154494200	Active TSS	Rectal Mucosa Donor 29	rectum
28	chrX:154493600-154494200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chrX:154493600-154494200	Active TSS	Brain Germinal Matrix	brain
30	chrX:154493800-154494400	Flanking Active TSS	Dnd41	blood
31	chrX:154494000-154494200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
32	chrX:154494000-154494200	Enhancers	Primary T cells from cord blood	blood
33	chrX:154494000-154494200	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chrX:154494000-154494200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chrX:154494000-154494200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chrX:154494000-154494200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chrX:154494000-154494200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chrX:154494000-154494200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chrX:154494000-154494200	Enhancers	A549	lung

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