Variant report

Variant	rs480210
Chromosome Location	chrX:154446014-154446015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chrX:154439521..154442406-chrX:154443106..154447353,6	K562	blood:
2	chrX:154438442..154440385-chrX:154445237..154447787,2	MCF-7	breast:
3	chrX:154444639..154446602-chrX:154492705..154495023,2	MCF-7	breast:
4	chrX:154299870..154302217-chrX:154444553..154446878,2	MCF-7	breast:
5	chrX:154440008..154442406-chrX:154443755..154447353,4	K562	blood:
6	chrX:154441104..154443352-chrX:154443765..154447008,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185515	Chromatin interaction
ENSG00000224978	Chromatin interaction
ENSG00000155961	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11156600	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap]
rs11887	0.87[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap]
rs12013168	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1393999	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2051161	0.87[ASW][hapmap]
rs3105275	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs3105276	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs35296872	0.91[CHB][hapmap];0.94[MEX][hapmap]
rs4893113	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs492622	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap]
rs496740	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs499428	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs499669	0.87[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap]
rs504984	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs507127	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs516396	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs519641	1.00[CHB][hapmap]
rs520145	1.00[CHB][hapmap]
rs523614	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs524609	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs525161	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap]
rs533001	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs542899	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs543054	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs544582	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs547724	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs559165	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs568396	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs573189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs573572	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs5945282	1.00[ASW][hapmap]
rs5983697	0.91[CHB][hapmap]
rs5983764	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6567813	0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[MEX][hapmap]
rs6649625	1.00[LWK][hapmap];0.81[MKK][hapmap]
rs782769	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs965691	0.87[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916671	chrX:154418093-154560374	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv532966	chrX:154418093-154721378	Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv29972	chrX:154418093-154929412	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv532965	chrX:154418093-155226096	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv532967	chrX:154418093-155252027	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154443800-154446400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chrX:154443800-154446400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chrX:154443800-154446400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chrX:154443800-154446400	Active TSS	HSMMtube	muscle
5	chrX:154444000-154446200	Active TSS	H1 Cell Line	embryonic stem cell
6	chrX:154444000-154446200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chrX:154444000-154446200	Active TSS	Brain Anterior Caudate	brain
8	chrX:154444000-154446200	Active TSS	HSMM	muscle
9	chrX:154444000-154446400	Active TSS	H9 Cell Line	embryonic stem cell
10	chrX:154444000-154446400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chrX:154444000-154446400	Active TSS	Muscle Satellite Cultured Cells	--
12	chrX:154444000-154446400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chrX:154444000-154446400	Active TSS	Stomach Smooth Muscle	stomach
14	chrX:154444000-154446400	Active TSS	HMEC	breast
15	chrX:154444000-154446600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chrX:154444000-154446600	Active TSS	Fetal Brain Female	brain
17	chrX:154444000-154447200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chrX:154444200-154446200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chrX:154444200-154446200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chrX:154444200-154446200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chrX:154444200-154446400	Active TSS	Right Atrium	heart
22	chrX:154444200-154446400	Active TSS	NHLF	lung
23	chrX:154444400-154446400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chrX:154444400-154446400	Active TSS	A549	lung
25	chrX:154444800-154446200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chrX:154445000-154460600	Weak transcription	Stomach Mucosa	stomach
27	chrX:154445200-154446200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chrX:154445200-154446400	Flanking Active TSS	Liver	Liver
29	chrX:154445400-154446200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chrX:154445400-154465400	Weak transcription	Spleen	Spleen
31	chrX:154445600-154446200	Enhancers	Primary B cells from peripheral blood	blood
32	chrX:154445600-154446200	Enhancers	Adipose Nuclei	Adipose
33	chrX:154445600-154446200	Enhancers	Colon Smooth Muscle	Colon
34	chrX:154445600-154446400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chrX:154445600-154446400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chrX:154445600-154446400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chrX:154445600-154446400	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chrX:154445600-154446400	Enhancers	Fetal Intestine Large	intestine
39	chrX:154445600-154446400	Flanking Active TSS	HUVEC	blood vessel
40	chrX:154445600-154446600	Enhancers	Primary B cells from cord blood	blood
41	chrX:154445600-154447000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chrX:154445600-154447200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chrX:154445600-154447200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chrX:154445600-154447600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chrX:154445600-154449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chrX:154445600-154449200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chrX:154445600-154449400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chrX:154445600-154456200	Weak transcription	Left Ventricle	heart
49	chrX:154445600-154456400	Weak transcription	Rectal Smooth Muscle	rectum
50	chrX:154445600-154465000	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links