Variant report

Variant	rs5945100
Chromosome Location	chrX:153738092-153738093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chrX:153737836-153738100	K562	blood:	n/a	n/a
2	SETDB1	chrX:153737689-153738188	U2OS	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	X:153657611-153671976..X:153736289-153755323	Hela-S3	cervix:
2	chrX:153625197..153632179-chrX:153731627..153740154,10	K562	blood:
3	X:153614328-153625659..X:153736289-153755323	GM12878	blood:
4	chrX:153734028..153735956-chrX:153736042..153738423,2	MCF-7	breast:
5	chrX:153717480..153721487-chrX:153737421..153739589,3	MCF-7	breast:
6	chrX:153733316..153735790-chrX:153736170..153738278,2	MCF-7	breast:

No data

Variant related genes	Relation type
FAM3A	TF binding region
ENSG00000071553	Chromatin interaction
ENSG00000126903	Chromatin interaction
ENSG00000071889	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000013563	Chromatin interaction
ENSG00000203879	Chromatin interaction
ENSG00000147403	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1050047	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs12392447	0.90[CEU][hapmap]
rs17052003	0.90[CEU][hapmap];0.83[CHD][hapmap];0.85[TSI][hapmap]
rs2071429	0.82[CEU][hapmap]
rs2315325	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs2472393	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs2472394	0.90[CEU][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap]
rs4542114	0.84[JPT][hapmap]
rs4898389	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs5945195	0.90[CEU][hapmap]
rs5945218	0.90[CEU][hapmap];0.83[CHD][hapmap];0.85[TSI][hapmap]
rs5945429	0.82[CEU][hapmap]
rs5945431	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs5945433	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs5986981	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs5987266	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs5987267	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs7051615	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs7057286	0.82[CEU][hapmap];0.84[JPT][hapmap]
rs7611	1.00[CHB][hapmap]
rs7879049	0.90[CEU][hapmap];0.83[CHD][hapmap];0.85[TSI][hapmap]
rs7886727	0.82[CEU][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33199	chrX:152864376-153820241	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	276 gene(s)	inside rSNPs	diseases
2	nsv528291	chrX:152864376-153827637	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	277 gene(s)	inside rSNPs	diseases
3	nsv915605	chrX:153333946-153783638	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	nsv519042	chrX:153348431-153829693	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv532962	chrX:153564946-153870337	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	199 gene(s)	inside rSNPs	diseases
6	nsv532963	chrX:153576890-153822717	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	195 gene(s)	inside rSNPs	diseases
7	nsv530281	chrX:153622940-153783184	Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
8	nsv532964	chrX:153622940-153854307	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
9	nsv995104	chrX:153731421-153832724	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5945100	LAGE3	cis	lymphoblastoid	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153726200-153743200	Weak transcription	Primary B cells from cord blood	blood
2	chrX:153730000-153743400	Weak transcription	Hela-S3	cervix
3	chrX:153730200-153739400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chrX:153731200-153739400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chrX:153731200-153739400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chrX:153731200-153743400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chrX:153731800-153743400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chrX:153731800-153743600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chrX:153732000-153743600	Weak transcription	Small Intestine	intestine
10	chrX:153732400-153743400	Weak transcription	Rectal Smooth Muscle	rectum
11	chrX:153733200-153740000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chrX:153733400-153738200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chrX:153733400-153738200	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chrX:153733400-153738400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chrX:153733400-153738400	Strong transcription	Fetal Intestine Large	intestine
16	chrX:153733400-153738600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chrX:153733400-153739000	ZNF genes & repeats	Fetal Stomach	stomach
18	chrX:153733400-153742200	Weak transcription	Stomach Mucosa	stomach
19	chrX:153733600-153738600	Strong transcription	Thymus	Thymus
20	chrX:153733600-153739200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chrX:153733600-153742600	Strong transcription	Fetal Intestine Small	intestine
22	chrX:153733800-153738600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chrX:153734000-153743600	Weak transcription	Psoas Muscle	Psoas
24	chrX:153734400-153738200	ZNF genes & repeats	Placenta	Placenta
25	chrX:153734400-153738200	Strong transcription	Right Ventricle	heart
26	chrX:153734600-153743400	Weak transcription	Osteobl	bone
27	chrX:153734600-153743600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chrX:153734800-153741200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chrX:153734800-153743400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chrX:153734800-153743400	Weak transcription	HSMM	muscle
31	chrX:153734800-153743600	Weak transcription	HSMMtube	muscle
32	chrX:153734800-153743600	Weak transcription	NH-A	brain
33	chrX:153735000-153738200	ZNF genes & repeats	Adipose Nuclei	Adipose
34	chrX:153735000-153739000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chrX:153735400-153738400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chrX:153735400-153740000	Weak transcription	Dnd41	blood
37	chrX:153735600-153738600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chrX:153735600-153739600	Weak transcription	K562	blood
39	chrX:153735600-153743600	Weak transcription	Left Ventricle	heart
40	chrX:153735800-153738200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chrX:153735800-153743400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chrX:153735800-153743600	Weak transcription	Esophagus	oesophagus
43	chrX:153735800-153743800	Weak transcription	Aorta	Aorta
44	chrX:153736000-153738200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chrX:153736000-153738600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chrX:153736000-153739400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chrX:153736000-153739600	Weak transcription	Primary hematopoietic stem cells	blood
48	chrX:153736000-153739800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chrX:153736000-153740000	Strong transcription	Fetal Muscle Trunk	muscle
50	chrX:153736000-153741600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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