Variant report

Variant	rs11079429
Chromosome Location	chr17:59472403-59472404
allele	A/G
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	GATA3	chr17:59470148-59472995	MCF-7	breast:	n/a	chr17:59471848-59471857
2	POLR2A	chr17:59468390-59479830	ProgFib	skin:	n/a	n/a
3	TEAD4	chr17:59466501-59473617	A549	lung:	n/a	n/a
4	MAZ	chr17:59470841-59472805	IMR90	lung:	n/a	n/a
5	CTCF	chr17:59472320-59472470	GM12874	blood:	n/a	n/a
6	RAD21	chr17:59464232-59473165	MCF-7	breast:	n/a	chr17:59469180-59469190 chr17:59469147-59469157 chr17:59471166-59471180 chr17:59467970-59467984 chr17:59467474-59467493 chr17:59471160-59471173 chr17:59468503-59468516 chr17:59465088-59465102 chr17:59471168-59471187 chr17:59464507-59464519 chr17:59471513-59471526 chr17:59470903-59470917 chr17:59466182-59466196 chr17:59472703-59472713 chr17:59469179-59469192
7	POLR2A	chr17:59472310-59473000	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr17:59472168-59472572	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr17:59472298-59472863	HepG2	liver:	n/a	n/a
10	POLR2A	chr17:59471162-59472873	HepG2	liver:	n/a	n/a
11	POLR2A	chr17:59468021-59474379	Hela-S3	cervix:	n/a	n/a
12	MYBL2	chr17:59470850-59472680	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:59469164..59471645-chr17:59472250..59474321,2	K562	blood:
2	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
3	chr17:57914760..57924876-chr17:59472133..59480361,28	MCF-7	breast:
4	chr17:57917973..57919820-chr17:59471106..59472896,2	MCF-7	breast:
5	chr17:59468937..59480240-chr20:49340039..49356868,49	MCF-7	breast:
6	chr17:59468469..59482635-chr20:45977748..45992950,51	MCF-7	breast:
7	chr17:56706858..56710627-chr17:59472052..59479583,11	MCF-7	breast:
8	chr17:56736472..56738107-chr17:59470143..59472768,3	MCF-7	breast:
9	chr17:59470592..59472862-chr9:115912081..115913641,2	MCF-7	breast:
10	chr17:59471714..59474637-chr20:45985553..45987667,2	MCF-7	breast:
11	chr17:59472370..59473091-chr20:49411016..49411529,2	MCF-7	breast:
12	chr17:59471895..59472416-chr20:49410876..49411525,2	MCF-7	breast:
13	chr17:59470525..59474011-chr17:59486288..59490375,89	MCF-7	breast:
14	chr17:57914768..57917622-chr17:59471234..59472961,2	MCF-7	breast:
15	chr17:59470522..59472690-chr20:55839093..55841752,2	MCF-7	breast:
16	chr17:59468167..59483990-chr20:49341590..49352501,35	MCF-7	breast:
17	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NACA2-2	chr17:59470242-59472935	ucscGeneNc_uc002jdy_1

Variant related genes	Relation type
ENSG00000267280	TF binding region
TBX2	TF binding region
ENSG00000101144	Chromatin interaction
ENSG00000136867	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000273451	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11871637	0.81[MEX][hapmap]
rs12952625	0.84[AMR][1000 genomes]
rs2270114	0.86[AMR][1000 genomes]
rs2286526	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs34446110	0.81[AMR][1000 genomes]
rs8068318	0.81[MEX][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	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	nsv518130	chr17:59456589-59491281	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	265 gene(s)	inside rSNPs	diseases
5	esv1796927	chr17:59460119-59495319	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	270 gene(s)	inside rSNPs	diseases
6	nsv908663	chr17:59464069-59521310	Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	278 gene(s)	inside rSNPs	diseases
7	nsv908664	chr17:59465697-59491030	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	261 gene(s)	inside rSNPs	diseases
8	nsv908665	chr17:59470193-59494574	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
9	nsv908666	chr17:59470842-59489822	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	253 gene(s)	inside rSNPs	diseases
10	nsv908667	chr17:59471151-59491030	Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	256 gene(s)	inside rSNPs	diseases
11	nsv908668	chr17:59471151-59494574	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	263 gene(s)	inside rSNPs	diseases
12	nsv908669	chr17:59471372-59491030	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
13	nsv908670	chr17:59471372-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	262 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11079429	NACA2	cis	cerebellum	SCAN
rs11079429	TMEM100	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59444600-59473400	Weak transcription	Right Atrium	heart
2	chr17:59447000-59473400	Weak transcription	Pancreas	Pancrea
3	chr17:59464000-59474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr17:59467400-59474000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr17:59467600-59472800	Weak transcription	Adipose Nuclei	Adipose
6	chr17:59467800-59472800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr17:59467800-59473800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:59470600-59472800	Enhancers	Hela-S3	cervix
9	chr17:59470600-59473600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr17:59470800-59472800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr17:59470800-59473200	Enhancers	Placenta	Placenta
12	chr17:59470800-59476000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr17:59471000-59472800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
14	chr17:59471000-59473200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:59471200-59472800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:59471200-59472800	Flanking Active TSS	HepG2	liver
17	chr17:59471200-59472800	Enhancers	NHDF-Ad	bronchial
18	chr17:59471200-59473400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr17:59471400-59472600	Enhancers	NH-A	brain
20	chr17:59471400-59474000	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr17:59471600-59472600	Weak transcription	Brain Substantia Nigra	brain
22	chr17:59471600-59472800	Bivalent Enhancer	Fetal Stomach	stomach
23	chr17:59471800-59473200	Weak transcription	Ovary	ovary
24	chr17:59471800-59475400	Weak transcription	A549	lung
25	chr17:59472000-59472600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:59472000-59473000	Flanking Active TSS	NHLF	lung
27	chr17:59472000-59474000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:59472200-59472600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:59472200-59472600	Flanking Active TSS	Fetal Lung	lung
30	chr17:59472200-59473600	Weak transcription	Osteobl	bone
31	chr17:59472200-59474000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr17:59472200-59475000	Weak transcription	HSMM	muscle
33	chr17:59472400-59472600	Enhancers	Esophagus	oesophagus
34	chr17:59472400-59472600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
35	chr17:59472400-59473200	Enhancers	Lung	lung
36	chr17:59472400-59473200	ZNF genes & repeats	Spleen	Spleen
37	chr17:59472400-59474000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr17:59472400-59474000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:59472400-59474200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain

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