Variant report

Variant	rs17428
Chromosome Location	chrX:153609963-153609964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chrX:153606771..153611068-chrX:153656465..153659469,5	MCF-7	breast:
2	chrX:153595264..153612826-chrX:153621461..153634267,75	MCF-7	breast:
3	chrX:153605609..153613633-chrX:153623295..153631024,31	K562	blood:
4	chrX:153609340..153611952-chrX:153757167..153759082,2	MCF-7	breast:
5	chrX:153606962..153610792-chrX:153771675..153776389,4	MCF-7	breast:
6	chrX:153605422..153612399-chrX:153623295..153634357,29	K562	blood:
7	chrX:153594620..153614384-chrX:153624179..153643019,157	MCF-7	breast:
8	chrX:153609948..153612033-chrX:153638346..153640500,2	K562	blood:
9	chrX:153609938..153613123-chrX:153714886..153717092,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000013563	Chromatin interaction
ENSG00000147403	Chromatin interaction
ENSG00000160211	Chromatin interaction
ENSG00000102125	Chromatin interaction
ENSG00000102178	Chromatin interaction
ENSG00000073009	Chromatin interaction
ENSG00000197180	Chromatin interaction
ENSG00000207165	Chromatin interaction
ENSG00000071553	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12007167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs17426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs2070822	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs2239470	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2872817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs4446899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs4898478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4898479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5945185	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs5945413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs5945423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs915943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531227	chrX:152864376-153655730	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv932632	chrX:153333946-153623000	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv531232	chrX:153333946-153626120	Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv531233	chrX:153333946-153626120	Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv523072	chrX:153333946-153626738	Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv9999	chrX:153567427-153621413	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
12	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
13	nsv817569	chrX:153592317-153634020	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	151 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153606200-153610000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chrX:153606200-153610000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chrX:153608200-153613400	ZNF genes & repeats	Fetal Stomach	stomach
4	chrX:153608400-153610000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
5	chrX:153608600-153610000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chrX:153608600-153611400	Weak transcription	Small Intestine	intestine
7	chrX:153608800-153610000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chrX:153608800-153610400	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
9	chrX:153608800-153610400	Weak transcription	Fetal Kidney	kidney
10	chrX:153608800-153612800	Weak transcription	Fetal Lung	lung
11	chrX:153609000-153610000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chrX:153609000-153610200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chrX:153609000-153610400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chrX:153609000-153612200	Weak transcription	Brain Cingulate Gyrus	brain
15	chrX:153609000-153612400	Weak transcription	Ovary	ovary
16	chrX:153609000-153612800	Weak transcription	Brain Substantia Nigra	brain
17	chrX:153609000-153612800	Weak transcription	Psoas Muscle	Psoas
18	chrX:153609000-153612800	Weak transcription	Right Atrium	heart
19	chrX:153609000-153618600	Weak transcription	Thymus	Thymus
20	chrX:153609200-153610000	Enhancers	NH-A	brain
21	chrX:153609200-153610400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chrX:153609200-153610400	Strong transcription	NHEK	skin
23	chrX:153609200-153611200	Strong transcription	Osteobl	bone
24	chrX:153609200-153612000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chrX:153609200-153612000	Weak transcription	Stomach Mucosa	stomach
26	chrX:153609200-153612600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chrX:153609200-153612800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chrX:153609200-153612800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chrX:153609200-153612800	Weak transcription	Primary B cells from cord blood	blood
30	chrX:153609200-153612800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chrX:153609200-153612800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chrX:153609200-153612800	Weak transcription	Left Ventricle	heart
33	chrX:153609200-153613000	Weak transcription	Primary T cells from cord blood	blood
34	chrX:153609200-153613000	Weak transcription	Brain Angular Gyrus	brain
35	chrX:153609400-153610000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chrX:153609400-153610000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chrX:153609400-153610000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chrX:153609400-153610000	Genic enhancers	A549	lung
39	chrX:153609400-153610200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chrX:153609400-153610200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chrX:153609400-153610200	Strong transcription	Fetal Intestine Large	intestine
42	chrX:153609400-153610200	Enhancers	Hela-S3	cervix
43	chrX:153609400-153610400	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chrX:153609400-153610400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chrX:153609400-153610400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chrX:153609400-153610400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chrX:153609400-153610400	Strong transcription	Adipose Nuclei	Adipose
48	chrX:153609400-153610400	Strong transcription	Fetal Muscle Trunk	muscle
49	chrX:153609400-153610400	Strong transcription	Dnd41	blood
50	chrX:153609400-153610600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links