Variant report

Variant	rs12559
Chromosome Location	chrX:153630293-153630294
allele	A/G
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:53)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:53 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:153624383..153633652-chrX:153704408..153721325,48	MCF-7	breast:
2	chr6:35435616..35437664-chrX:153627963..153630833,2	K562	blood:
3	chrX:153625463..153630462-chrX:153744222..153748220,7	K562	blood:
4	chr14:35590604..35591439-chrX:153629748..153630313,2	Hela-S3	cervix:
5	chr1:154570743..154573459-chrX:153628802..153631031,2	K562	blood:
6	X:153625659-153635385..X:153719993-153730954	GM12878	blood:
7	chrX:153624019..153633071-chrX:153652023..153663795,26	MCF-7	breast:
8	chrX:153625830..153633897-chrX:153767392..153772063,11	K562	blood:
9	chrX:153628686..153631914-chrX:153723299..153726261,3	K562	blood:
10	chrX:153625623..153631615-chrX:153684928..153690706,13	K562	blood:
11	chr17:39974908..39976615-chrX:153629052..153631273,2	K562	blood:
12	chrX:153629830..153632179-chrX:153734126..153736368,2	K562	blood:
13	chrX:153625525..153632382-chrX:153663983..153668753,13	K562	blood:
14	chrX:153582162..153585045-chrX:153627001..153630604,4	K562	blood:
15	X:153625659-153635385..X:154053104-154056925	GM12878	blood:
16	chrX:153629459..153632266-chrX:153773289..153775719,2	K562	blood:
17	chrX:153594250..153603496-chrX:153624447..153635089,39	K562	blood:
18	chrX:153586879..153589611-chrX:153629285..153631493,3	K562	blood:
19	chrX:153624542..153632362-chrX:153710560..153721332,23	K562	blood:
20	chr12:54678561..54680641-chrX:153629578..153632239,2	K562	blood:
21	chrX:153592401..153602834-chrX:153624077..153632705,30	K562	blood:
22	chrX:153586062..153591083-chrX:153626549..153633665,7	K562	blood:
23	chrX:153626135..153631801-chrX:153703936..153709269,13	K562	blood:
24	chrX:153625254..153633054-chrX:153663966..153667311,10	MCF-7	breast:
25	X:153625659-153635385..X:153657611-153671976	H1-hESC	embryonic stem cell:	embryo
26	chr6:26214292..26216427-chrX:153629592..153631325,2	MCF-7	breast:
27	chrX:153625628..153632278-chrX:153692369..153698999,8	K562	blood:
28	chrX:153628496..153632066-chrX:153744718..153747397,4	K562	blood:
29	chrX:153629608..153631581-chrX:153679580..153681863,2	K562	blood:
30	X:153625659-153635385..X:154119150-154130142	GM12878	blood:
31	X:153625659-153635385..X:154140465-154148278	K562	blood:
32	chr20:42086383..42086967-chrX:153629748..153630369,2	Hela-S3	cervix:
33	chrX:153625197..153632179-chrX:153731627..153740154,10	K562	blood:
34	chrX:153624545..153632466-chrX:153709449..153721332,27	K562	blood:
35	chr20:632233..634928-chrX:153628055..153630928,2	K562	blood:
36	chrX:153629574..153632888-chrX:153673658..153677156,4	MCF-7	breast:
37	chrX:153624619..153634737-chrX:153752670..153765167,48	K562	blood:
38	chrX:153624391..153630513-chrX:153767458..153777755,28	MCF-7	breast:
39	chrX:153629889..153630747-chrX:153762429..153763052,2	MCF-7	breast:
40	chrX:153594620..153614384-chrX:153624179..153643019,157	MCF-7	breast:
41	chrX:153605609..153613633-chrX:153623295..153631024,31	K562	blood:
42	chrX:153625412..153631801-chrX:153757258..153764804,13	MCF-7	breast:
43	chrX:153624495..153633022-chrX:153668916..153678988,23	K562	blood:
44	chr6:32115974..32117964-chrX:153629530..153631311,2	MCF-7	breast:
45	chrX:153624951..153633171-chrX:153753466..153766700,56	K562	blood:
46	chrX:153624950..153633168-chrX:153684275..153690571,17	MCF-7	breast:
47	chrX:153595264..153612826-chrX:153621461..153634267,75	MCF-7	breast:
48	chrX:153624413..153633458-chrX:153703786..153709269,18	K562	blood:
49	chr6:26054762..26057437-chrX:153628983..153631256,2	K562	blood:
50	chrX:153625816..153632596-chrX:153691104..153698525,12	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196924	Chromatin interaction
ENSG00000224069	Chromatin interaction
ENSG00000092020	Chromatin interaction
ENSG00000264484	Chromatin interaction
ENSG00000141756	Chromatin interaction
ENSG00000073009	Chromatin interaction
ENSG00000261773	Chromatin interaction
ENSG00000197180	Chromatin interaction
ENSG00000071553	Chromatin interaction
ENSG00000203870	Chromatin interaction
ENSG00000196976	Chromatin interaction
ENSG00000264783	Chromatin interaction
ENSG00000198755	Chromatin interaction
ENSG00000160211	Chromatin interaction
ENSG00000071889	Chromatin interaction
ENSG00000126903	Chromatin interaction
ENSG00000237859	Chromatin interaction
ENSG00000071859	Chromatin interaction
ENSG00000124193	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000203879	Chromatin interaction
ENSG00000102119	Chromatin interaction
ENSG00000130827	Chromatin interaction
ENSG00000271086	Chromatin interaction
ENSG00000204314	Chromatin interaction
ENSG00000271303	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000102178	Chromatin interaction
ENSG00000264631	Chromatin interaction
ENSG00000100890	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1130929	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12007167	1.00[YRI][hapmap]
rs12877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2051508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070643	0.88[JPT][hapmap]
rs2070807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2070829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2097214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2156911	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2239469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2283762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28602900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4898484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4898494	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6727	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs743547	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs743548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs743549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs762514	1.00[CEU][hapmap]
rs7886627	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs915941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs915942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:153625400-153631600	ZNF genes & repeats	Fetal Brain Female	brain
2	chrX:153627200-153637200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chrX:153627600-153630800	Strong transcription	Spleen	Spleen
4	chrX:153628000-153634000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chrX:153628000-153636800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chrX:153628200-153630400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chrX:153628200-153633200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chrX:153628200-153639600	Weak transcription	Small Intestine	intestine
9	chrX:153628400-153637200	Weak transcription	Primary T cells from cord blood	blood
10	chrX:153628400-153639400	Weak transcription	Ovary	ovary
11	chrX:153628600-153630400	Genic enhancers	Fetal Intestine Large	intestine
12	chrX:153628600-153630800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chrX:153628600-153631000	Strong transcription	Primary B cells from peripheral blood	blood
14	chrX:153628600-153633800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chrX:153628600-153636600	Weak transcription	Psoas Muscle	Psoas
16	chrX:153628600-153636800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chrX:153628600-153637000	Weak transcription	Primary B cells from cord blood	blood
18	chrX:153628600-153637000	Weak transcription	Primary hematopoietic stem cells	blood
19	chrX:153628600-153637000	Weak transcription	Colon Smooth Muscle	Colon
20	chrX:153628600-153639400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chrX:153628800-153630400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chrX:153628800-153630400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chrX:153628800-153630600	Strong transcription	Fetal Thymus	thymus
24	chrX:153628800-153631000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chrX:153628800-153631000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
26	chrX:153628800-153631200	Strong transcription	Brain Germinal Matrix	brain
27	chrX:153628800-153631400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chrX:153628800-153632000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chrX:153628800-153633400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chrX:153628800-153636600	Weak transcription	Brain Cingulate Gyrus	brain
31	chrX:153628800-153637000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chrX:153628800-153637000	Weak transcription	Stomach Mucosa	stomach
33	chrX:153628800-153637400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chrX:153628800-153637600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chrX:153628800-153639400	Weak transcription	Fetal Lung	lung
36	chrX:153629000-153631600	Strong transcription	Duodenum Mucosa	Duodenum
37	chrX:153629000-153634000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chrX:153629000-153637000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chrX:153629200-153630600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chrX:153629200-153630600	Genic enhancers	Fetal Intestine Small	intestine
41	chrX:153629200-153639400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chrX:153629400-153630400	Strong transcription	Brain Hippocampus Middle	brain
43	chrX:153629400-153636600	Weak transcription	Hela-S3	cervix
44	chrX:153629600-153630400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chrX:153629600-153630400	Strong transcription	Gastric	stomach
46	chrX:153629600-153630400	Genic enhancers	A549	lung
47	chrX:153629600-153630400	Enhancers	HepG2	liver
48	chrX:153629600-153631200	Weak transcription	Right Ventricle	heart
49	chrX:153629600-153632200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chrX:153629600-153636600	Weak transcription	HSMMtube	muscle

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