Variant report

Variant	rs3848900
Chromosome Location	chrX:65238011-65238012
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	POLR2A	chrX:65234004-65243893	K562	blood:	n/a	n/a
2	IRF1	chrX:65237862-65239164	K562	blood:	n/a	chrX:65238568-65238577 chrX:65238687-65238696 chrX:65238033-65238046 chrX:65238924-65238933
3	POLR2A	chrX:65237796-65238070	K562	blood:	n/a	n/a
4	TBL1XR1	chrX:65234590-65243407	K562	blood:	n/a	n/a
5	POLR2A	chrX:65234870-65239435	K562	blood:	n/a	n/a
6	POLR2A	chrX:65234515-65244251	K562	blood:	n/a	n/a
7	POLR2A	chrX:65234927-65244173	K562	blood:	n/a	n/a
8	POLR2A	chrX:65234135-65246356	NB4	blood:	n/a	n/a
9	POLR2A	chrX:65234453-65243909	K562	blood:	n/a	n/a
10	ZMIZ1	chrX:65237364-65239953	K562	blood:	n/a	n/a
11	POLR2A	chrX:65234363-65244036	K562	blood:	n/a	n/a
12	HEY1	chrX:65237833-65239523	K562	blood:	n/a	chrX:65238630-65238639
13	POLR2A	chrX:65234921-65239429	GM12892	blood:	n/a	n/a
14	POLR2A	chrX:65234932-65239158	GM19099	blood:	n/a	n/a
15	PML	chrX:65237879-65239153	K562	blood:	n/a	chrX:65238416-65238424
16	MAZ	chrX:65237860-65239118	K562	blood:	n/a	n/a
17	POLR2A	chrX:65234813-65239253	GM18505	blood:	n/a	n/a
18	PML	chrX:65237785-65239472	K562	blood:	n/a	chrX:65238416-65238424
19	POLR2A	chrX:65235007-65239030	GM12878	blood:	n/a	n/a
20	CUX1	chrX:65236387-65239429	K562	blood:	n/a	n/a
21	POLR2A	chrX:65234921-65239175	K562	blood:	n/a	n/a
22	UBTF	chrX:65234619-65239721	K562	blood:	n/a	n/a
23	HEY1	chrX:65236580-65238106	K562	blood:	n/a	n/a
24	POLR2A	chrX:65234498-65243895	K562	blood:	n/a	n/a
25	POLR2A	chrX:65234449-65243604	HL-60	blood:	n/a	n/a
26	POLR2A	chrX:65231192-65243901	GM12891	blood:	n/a	n/a
27	POLR2A	chrX:65231803-65243685	HL-60	blood:	n/a	n/a
28	TEAD4	chrX:65234874-65239286	K562	blood:	n/a	n/a
29	MAFK	chrX:65236012-65238323	K562	blood:	n/a	n/a
30	POLR2A	chrX:65234741-65239877	PBDE	blood:	n/a	n/a
31	TAF7	chrX:65234995-65238026	K562	blood:	n/a	n/a
32	POLR2A	chrX:65234508-65246309	K562	blood:	n/a	n/a
33	IRF1	chrX:65237861-65239414	K562	blood:	n/a	chrX:65238568-65238577 chrX:65238687-65238696 chrX:65238033-65238046 chrX:65238924-65238933

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:65236761..65240067-chrX:65380699..65383894,4	K562	blood:

Variant related genes	Relation type
MIR223	TF binding region
ENSG00000089472	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1028348	0.86[MEX][hapmap]
rs1325561	0.93[MEX][hapmap]
rs3848893	0.93[YRI][hapmap]
rs3848897	1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap]
rs3848901	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs3903921	0.90[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs3903922	1.00[CEU][hapmap]
rs4827449	0.93[MEX][hapmap];0.84[TSI][hapmap]
rs582787	0.86[MEX][hapmap];1.00[TSI][hapmap]
rs585069	0.93[MEX][hapmap];1.00[TSI][hapmap]
rs586789	0.93[MEX][hapmap];1.00[TSI][hapmap]
rs587657	0.93[MEX][hapmap];1.00[TSI][hapmap]
rs5918587	0.93[MEX][hapmap];0.92[TSI][hapmap]
rs5918974	0.93[MEX][hapmap];0.92[TSI][hapmap]
rs5964466	0.86[MEX][hapmap]
rs5964480	1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap]
rs5964482	1.00[ASW][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap]
rs5964483	1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap]
rs5964486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5964487	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs5964488	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs5964489	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs5965077	1.00[ASW][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap]
rs5965083	0.89[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap]
rs5965084	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs5965085	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs5965087	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs606886	0.93[MEX][hapmap];0.92[TSI][hapmap]
rs6624823	1.00[CHD][hapmap]
rs6624844	0.93[MEX][hapmap];0.92[TSI][hapmap]
rs670546	0.93[MEX][hapmap];1.00[TSI][hapmap]
rs760867	0.93[MEX][hapmap];0.84[TSI][hapmap]
rs7882859	1.00[CHD][hapmap]
rs9306698	1.00[CEU][hapmap]
rs9633155	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs9887348	1.00[CEU][hapmap]

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	esv3429625	chrX:64787230-65458721	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv995042	chrX:65121634-65953299	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active 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	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:65231800-65239000	Enhancers	Fetal Thymus	thymus
2	chrX:65231800-65244000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chrX:65232000-65239000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chrX:65234200-65241800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chrX:65235000-65238200	Active TSS	Duodenum Mucosa	Duodenum
6	chrX:65235000-65239000	Flanking Active TSS	GM12878-XiMat	blood
7	chrX:65235400-65238600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chrX:65235400-65238800	Active TSS	Brain Hippocampus Middle	brain
9	chrX:65235600-65238200	Active TSS	Placenta	Placenta
10	chrX:65235600-65238400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chrX:65235600-65238600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chrX:65235600-65239000	Enhancers	Primary T cells fromperipheralblood	blood
13	chrX:65235600-65241600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chrX:65235800-65238600	Enhancers	Dnd41	blood
15	chrX:65235800-65239200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chrX:65235800-65241800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chrX:65236000-65239000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chrX:65236400-65240800	Transcr. at gene 5' and 3'	K562	blood
19	chrX:65236400-65242000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chrX:65236600-65238200	Weak transcription	Spleen	Spleen
21	chrX:65236600-65239400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
22	chrX:65236600-65240200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
23	chrX:65237000-65239400	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chrX:65237000-65239800	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
25	chrX:65237200-65239400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chrX:65237400-65238400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
27	chrX:65237400-65238800	Flanking Active TSS	Primary B cells from cord blood	blood
28	chrX:65237600-65238800	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
29	chrX:65237600-65240400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chrX:65237800-65238200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chrX:65237800-65238800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
32	chrX:65237800-65239400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chrX:65237800-65241400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
34	chrX:65237800-65242000	Enhancers	Primary T cells from cord blood	blood

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