Variant report

Variant	rs1040407
Chromosome Location	chrX:78619827-78619828
allele	G/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	FOXA1	chrX:78619774-78620088	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ITM2A	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs13789	1.00[CEU][hapmap]
rs17317696	1.00[CHB][hapmap]
rs3761589	1.00[CHB][hapmap]
rs3761590	1.00[CHB][hapmap];0.82[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	esv3394349	chrX:77977388-78779139	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932683	chrX:78373033-79166725	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869186	chrX:78392001-79166725	Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv995120	chrX:78528055-78946146	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv519126	chrX:78586744-78629178	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv529913	chrX:78605903-79090819	Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:78611000-78620800	Weak transcription	Fetal Muscle Trunk	muscle
2	chrX:78616200-78620800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chrX:78616200-78620800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chrX:78616800-78621600	Weak transcription	Brain Angular Gyrus	brain
5	chrX:78617600-78620800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chrX:78617800-78620600	Weak transcription	K562	blood
7	chrX:78618000-78621800	Weak transcription	Left Ventricle	heart
8	chrX:78618400-78621000	Weak transcription	Fetal Stomach	stomach
9	chrX:78618600-78621400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chrX:78618600-78623200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chrX:78618600-78623200	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chrX:78618800-78620600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chrX:78618800-78620800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chrX:78618800-78620800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chrX:78618800-78621000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chrX:78618800-78623000	Active TSS	Primary T cells fromperipheralblood	blood
17	chrX:78618800-78623000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chrX:78619000-78623400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chrX:78619000-78623400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chrX:78619200-78622200	Active TSS	Fetal Muscle Leg	muscle
21	chrX:78619200-78623000	Active TSS	Fetal Thymus	thymus
22	chrX:78619200-78623400	Active TSS	Primary T cells from cord blood	blood
23	chrX:78619400-78623200	Active TSS	Primary T helper cells fromperipheralblood	blood
24	chrX:78619600-78620400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chrX:78619600-78621000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chrX:78619800-78620000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chrX:78619800-78620000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chrX:78619800-78620000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chrX:78619800-78620200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
30	chrX:78619800-78620200	Active TSS	Brain Substantia Nigra	brain
31	chrX:78619800-78621400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chrX:78619800-78623000	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chrX:78619800-78623000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chrX:78619800-78623200	Active TSS	Right Atrium	heart
35	chrX:78619800-78623200	Active TSS	Thymus	Thymus

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