Variant report

Variant	rs5955049
Chromosome Location	chrX:139006698-139006699
allele	A/C
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	CEBPB	chrX:139006453-139006709	K562	blood:	n/a	chrX:139006598-139006609
2	RCOR1	chrX:139006413-139006848	K562	blood:	n/a	n/a
3	EP300	chrX:139006242-139006712	SK-N-SH_RA	brain:	n/a	n/a
4	CEBPB	chrX:139006454-139006786	IMR90	lung:	n/a	chrX:139006598-139006609
5	PBX3	chrX:139006228-139007127	SK-N-SH	brain:	n/a	n/a
6	FOS	chrX:139006435-139006756	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chrX:139006423-139006770	HepG2	liver:	n/a	chrX:139006598-139006609

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:139006431..139009320-chrX:139009614..139012106,2	MCF-7	breast:
2	chrX:139003030..139006775-chrX:139014135..139016470,3	MCF-7	breast:

Variant related genes	Relation type
MIR505	TF binding region
ENSG00000101974	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10126150	1.00[YRI][hapmap]
rs12389012	1.00[YRI][hapmap]
rs12688688	0.81[YRI][hapmap]
rs17282011	0.86[YRI][hapmap]
rs1890241	1.00[YRI][hapmap]
rs5908152	1.00[YRI][hapmap]
rs5953748	0.81[YRI][hapmap]
rs5953790	0.86[YRI][hapmap]
rs5953791	1.00[YRI][hapmap]
rs5953812	1.00[YRI][hapmap]
rs5954540	1.00[YRI][hapmap]
rs5954556	1.00[YRI][hapmap]
rs5954768	1.00[YRI][hapmap]
rs5954897	1.00[YRI][hapmap]
rs5954997	1.00[YRI][hapmap]
rs6635927	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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138986200-139012200	Weak transcription	Fetal Intestine Small	intestine
2	chrX:138993600-139008600	Weak transcription	GM12878-XiMat	blood
3	chrX:138994000-139012600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chrX:138995400-139011000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chrX:138996200-139012000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chrX:138998600-139013200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chrX:139000000-139012200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chrX:139003000-139013000	Weak transcription	Fetal Heart	heart
9	chrX:139003000-139013200	Weak transcription	Psoas Muscle	Psoas
10	chrX:139003200-139011600	Weak transcription	K562	blood
11	chrX:139003400-139008800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chrX:139004400-139006800	Weak transcription	HepG2	liver
13	chrX:139004600-139006800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chrX:139004800-139006800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chrX:139005000-139013200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chrX:139005200-139006800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chrX:139005400-139006800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chrX:139005400-139008600	Enhancers	Liver	Liver
19	chrX:139005800-139006800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chrX:139005800-139007000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chrX:139005800-139009400	Enhancers	HUVEC	blood vessel
22	chrX:139006000-139006800	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chrX:139006000-139007000	Enhancers	Monocytes-CD14+_RO01746	blood
24	chrX:139006200-139006800	Enhancers	Primary T cells fromperipheralblood	blood
25	chrX:139006200-139006800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chrX:139006200-139006800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chrX:139006200-139007000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chrX:139006200-139007200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chrX:139006200-139007200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chrX:139006200-139007200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chrX:139006200-139008600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chrX:139006400-139006800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chrX:139006400-139006800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chrX:139006400-139006800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chrX:139006400-139006800	Enhancers	Duodenum Mucosa	Duodenum
36	chrX:139006400-139006800	Enhancers	Ovary	ovary
37	chrX:139006400-139009000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chrX:139006400-139012400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chrX:139006600-139006800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chrX:139006600-139006800	Enhancers	Colon Smooth Muscle	Colon
41	chrX:139006600-139007000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chrX:139006600-139012800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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