Variant report

Variant	rs5942899
Chromosome Location	chrX:109401419-109401420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chrX:109401033..109404404-chrX:109560260..109562002,3	MCF-7	breast:
2	chrX:109400697..109402253-chrX:109562749..109564981,2	MCF-7	breast:
3	chrX:109400494..109402860-chrX:109404600..109406859,2	MCF-7	breast:
4	chrX:109400313..109408301-chrX:109409149..109412366,7	K562	blood:

Variant related genes	Relation type
ENSG00000101935	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1623948	0.87[CHB][hapmap]
rs1770343	0.87[CHB][hapmap]
rs1774690	0.87[CHB][hapmap]
rs1774691	0.87[CHB][hapmap]
rs2066364	0.80[MKK][hapmap];1.00[YRI][hapmap]
rs2294504	1.00[LWK][hapmap]
rs2791640	0.87[CHB][hapmap]
rs2795991	0.87[CHB][hapmap]
rs2795992	0.87[CHB][hapmap]
rs2795993	0.87[CHB][hapmap]
rs2795994	0.87[CHB][hapmap]
rs2795995	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs5942909	1.00[LWK][hapmap]
rs946820	0.87[CHB][hapmap]
rs946821	0.87[CHB][hapmap]
rs946822	0.87[CHB][hapmap]
rs947592	1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3369563	chrX:109079631-109573656	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	142 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5942899	CXCL14	trans	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:109334000-109402600	Weak transcription	Primary B cells from cord blood	blood
2	chrX:109352400-109402400	Weak transcription	Primary B cells from peripheral blood	blood
3	chrX:109352400-109414000	Weak transcription	Dnd41	blood
4	chrX:109377600-109403400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chrX:109385800-109406800	Weak transcription	Gastric	stomach
6	chrX:109386400-109404000	Weak transcription	Right Ventricle	heart
7	chrX:109387800-109404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chrX:109387800-109411000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chrX:109388200-109418000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chrX:109389000-109404000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chrX:109389000-109416800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chrX:109389000-109418000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chrX:109389200-109414600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chrX:109389600-109405600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chrX:109389600-109423200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chrX:109389800-109401800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chrX:109389800-109402200	Weak transcription	GM12878-XiMat	blood
18	chrX:109389800-109402400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chrX:109389800-109403000	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chrX:109389800-109403000	Weak transcription	HMEC	breast
21	chrX:109389800-109404200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chrX:109389800-109404200	Weak transcription	Adipose Nuclei	Adipose
23	chrX:109389800-109415000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chrX:109389800-109418400	Weak transcription	Brain Anterior Caudate	brain
25	chrX:109389800-109431800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chrX:109390000-109401600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chrX:109390000-109404000	Weak transcription	Fetal Thymus	thymus
28	chrX:109390000-109404200	Weak transcription	NHEK	skin
29	chrX:109390200-109405000	Weak transcription	Hela-S3	cervix
30	chrX:109390400-109401800	Weak transcription	Fetal Stomach	stomach
31	chrX:109390400-109432000	Weak transcription	Primary hematopoietic stem cells	blood
32	chrX:109392800-109415000	Weak transcription	Primary T cells from cord blood	blood
33	chrX:109393000-109404000	Weak transcription	Left Ventricle	heart
34	chrX:109393400-109401600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chrX:109393400-109413200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chrX:109393600-109414800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chrX:109393800-109404800	Weak transcription	Fetal Intestine Small	intestine
38	chrX:109397000-109414600	Weak transcription	Duodenum Mucosa	Duodenum
39	chrX:109399000-109404000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chrX:109399000-109415000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chrX:109399400-109419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chrX:109399800-109401600	Strong transcription	A549	lung
43	chrX:109399800-109402600	Enhancers	K562	blood
44	chrX:109399800-109404200	Weak transcription	NH-A	brain
45	chrX:109400000-109401800	Enhancers	Psoas Muscle	Psoas
46	chrX:109400800-109415400	Weak transcription	Fetal Intestine Large	intestine
47	chrX:109401400-109402400	Enhancers	Monocytes-CD14+_RO01746	blood

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