Variant report

Variant	rs16988888
Chromosome Location	chrX:64820594-64820595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chrX:64815387..64817166-chrX:64818665..64820717,2	K562	blood:
2	chrX:64808739..64811485-chrX:64818680..64822444,3	K562	blood:
3	chrX:64820184..64822143-chrX:64915881..64917547,2	K562	blood:
4	chrX:64819950..64822308-chrX:65218113..65220764,2	K562	blood:
5	chrX:64814191..64818207-chrX:64819444..64823049,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MSN-1	chrX:64820542-64820630	ENSG00000231669

Variant related genes	Relation type
ENSG00000237311	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs5964989	0.95[YRI][hapmap]
rs5964990	0.95[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	nsv817451	chrX:64049597-64916072	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv3409088	chrX:64739187-64876813	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:64812000-64822400	Weak transcription	Ovary	ovary
2	chrX:64813200-64823800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chrX:64814800-64823000	Enhancers	Primary B cells from peripheral blood	blood
4	chrX:64815600-64821600	Enhancers	Primary T cells from cord blood	blood
5	chrX:64815800-64821000	Weak transcription	Placenta	Placenta
6	chrX:64815800-64822600	Weak transcription	Brain Angular Gyrus	brain
7	chrX:64816000-64821200	Weak transcription	Fetal Lung	lung
8	chrX:64816000-64821200	Weak transcription	Stomach Mucosa	stomach
9	chrX:64816200-64820600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chrX:64816200-64821400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chrX:64816200-64821400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chrX:64816200-64821400	Weak transcription	A549	lung
13	chrX:64816200-64824200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chrX:64816200-64824800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chrX:64816400-64821200	Weak transcription	Right Ventricle	heart
16	chrX:64816400-64821400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chrX:64816400-64821400	Weak transcription	Fetal Stomach	stomach
18	chrX:64816400-64821400	Weak transcription	HSMM	muscle
19	chrX:64816400-64822800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chrX:64816400-64823200	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chrX:64816600-64821200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chrX:64816800-64821000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chrX:64816800-64821000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chrX:64816800-64821000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chrX:64816800-64821000	Weak transcription	Fetal Thymus	thymus
26	chrX:64816800-64821000	Weak transcription	Osteobl	bone
27	chrX:64816800-64821200	Weak transcription	Small Intestine	intestine
28	chrX:64816800-64821200	Weak transcription	NH-A	brain
29	chrX:64816800-64821400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chrX:64816800-64821400	Weak transcription	HMEC	breast
31	chrX:64816800-64821400	Weak transcription	NHDF-Ad	bronchial
32	chrX:64816800-64821400	Weak transcription	NHEK	skin
33	chrX:64817000-64821400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chrX:64817200-64821200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chrX:64817200-64821200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chrX:64817400-64821000	Weak transcription	Lung	lung
37	chrX:64818600-64821400	Weak transcription	GM12878-XiMat	blood
38	chrX:64818600-64822800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chrX:64818600-64824400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chrX:64818600-64828400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chrX:64818800-64820800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chrX:64818800-64820800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chrX:64818800-64821000	Weak transcription	Primary B cells from cord blood	blood
44	chrX:64818800-64821000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chrX:64818800-64821200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chrX:64818800-64821400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chrX:64818800-64821400	Weak transcription	Dnd41	blood
48	chrX:64818800-64823000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chrX:64818800-64823200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chrX:64818800-64823400	Enhancers	Primary T cells fromperipheralblood	blood

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