Variant report

Variant	rs2497279
Chromosome Location	chrX:138992022-138992023
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	NFIC	chrX:138991803-138992304	GM12878	blood:	n/a	n/a
2	RUNX3	chrX:138991855-138992270	GM12878	blood:	n/a	n/a
3	FOXM1	chrX:138991862-138992248	GM12878	blood:	n/a	n/a
4	BATF	chrX:138991929-138992221	GM12878	blood:	n/a	chrX:138992047-138992055
5	BATF	chrX:138991924-138992186	GM12878	blood:	n/a	chrX:138992047-138992055
6	EP300	chrX:138991966-138992188	GM12878	blood:	n/a	n/a
7	TBL1XR1	chrX:138991977-138992133	GM12878	blood:	n/a	n/a
8	CUX1	chrX:138991987-138992106	GM12878	blood:	n/a	n/a
9	BHLHE40	chrX:138991933-138992236	GM12878	blood:	n/a	n/a
10	SPI1	chrX:138991910-138992093	GM12891	blood:	n/a	chrX:138991993-138992006
11	SPI1	chrX:138991872-138992142	GM12878	blood:	n/a	chrX:138991993-138992006
12	MXI1	chrX:138991910-138992076	GM12878	blood:	n/a	n/a
13	EP300	chrX:138991946-138992239	GM12878	blood:	n/a	n/a
14	RUNX3	chrX:138991899-138992329	GM12878	blood:	n/a	n/a
15	RCOR1	chrX:138991902-138992164	GM12878	blood:	n/a	n/a
16	IKZF1	chrX:138991868-138992233	GM12878	blood:	n/a	n/a
17	NFIC	chrX:138991751-138992223	GM12878	blood:	n/a	n/a
18	EP300	chrX:138991949-138992178	GM12878	blood:	n/a	n/a
19	EBF1	chrX:138991856-138992262	GM12878	blood:	n/a	n/a
20	MEF2A	chrX:138991888-138992196	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000252719	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12012817	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs17002234	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs2094702	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs2485726	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs2485730	1.00[YRI][hapmap]
rs2485736	1.00[YRI][hapmap]
rs2491008	0.87[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2491012	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs2497267	0.90[YRI][hapmap]
rs4239992	0.85[YRI][hapmap]
rs4824921	1.00[YRI][hapmap]
rs5908666	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7061310	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532936	chrX:138687855-139384681	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv491760	chrX:138780768-139283477	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
3	nsv917353	chrX:138912620-139283492	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138985600-138994000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chrX:138985600-138994600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chrX:138986200-139012200	Weak transcription	Fetal Intestine Small	intestine
4	chrX:138987400-138995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chrX:138988200-138993000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chrX:138988200-138993600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chrX:138988600-138998000	Weak transcription	Thymus	Thymus
8	chrX:138988600-139006200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chrX:138989400-138992200	Enhancers	Liver	Liver
10	chrX:138989800-138992400	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chrX:138990000-138992600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chrX:138990600-138993200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chrX:138990600-138993400	Weak transcription	NHDF-Ad	bronchial
14	chrX:138991400-138992400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chrX:138991400-138992800	Enhancers	Primary B cells from peripheral blood	blood
16	chrX:138991600-138992200	Enhancers	Primary B cells from cord blood	blood
17	chrX:138991600-138992200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chrX:138991600-138992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chrX:138991800-138992200	Enhancers	Colon Smooth Muscle	Colon
20	chrX:138992000-138992200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chrX:138992000-138992200	Active TSS	GM12878-XiMat	blood
22	chrX:138992000-138992200	Active TSS	Monocytes-CD14+_RO01746	blood
23	chrX:138992000-139006200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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