Variant report

Variant	rs4129397
Chromosome Location	chr9:115975644-115975645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115951377..115953931-chr9:115974239..115975925,2	MCF-7	breast:
2	chr9:115975066..115976588-chr9:115978815..115981431,2	MCF-7	breast:
3	chr9:115974346..115976683-chr9:115980205..115982463,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10123415	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10125992	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10513189	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10739388	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739390	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10739392	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10759633	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10759636	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759637	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817461	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10817468	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11792628	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4129395	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4129396	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4284098	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4560868	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4979223	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4979226	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6477998	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6477999	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7022397	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7038769	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7041615	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7850357	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7851395	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7859354	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4129397	CDC26	cis	Esophagus Mucosa	GTEx
rs4129397	CDC26	cis	Artery Aorta	GTEx
rs4129397	CDC26	cis	Esophagus Muscularis	GTEx
rs4129397	CDC26	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115923400-115976400	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr9:115936800-115982400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:115945400-115977200	Weak transcription	Stomach Mucosa	stomach
4	chr9:115945600-115982800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:115950600-115982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:115950800-115982800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:115951000-115982800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:115962800-115976800	Weak transcription	Small Intestine	intestine
9	chr9:115964000-115976000	Strong transcription	Fetal Brain Female	brain
10	chr9:115964000-115977000	Weak transcription	Psoas Muscle	Psoas
11	chr9:115964800-115979200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:115965200-115980800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:115965200-115982000	Weak transcription	Colonic Mucosa	Colon
14	chr9:115965200-115982000	Weak transcription	Fetal Brain Male	brain
15	chr9:115965200-115982200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr9:115965400-115980800	Weak transcription	Brain Angular Gyrus	brain
17	chr9:115969000-115982400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:115969400-115981800	Weak transcription	HSMM	muscle
19	chr9:115969600-115976000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr9:115969600-115977200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr9:115969600-115980800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr9:115969600-115980800	Weak transcription	HepG2	liver
23	chr9:115969600-115981600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:115969600-115982400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr9:115969600-115982400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:115970000-115982800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:115970400-115981800	Weak transcription	NH-A	brain
28	chr9:115970600-115981800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:115971600-115982000	Weak transcription	NHDF-Ad	bronchial
30	chr9:115971800-115981000	Weak transcription	NHEK	skin
31	chr9:115971800-115982000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:115972000-115980800	Weak transcription	Osteobl	bone
33	chr9:115972400-115976600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:115972400-115981200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:115972400-115981200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr9:115972400-115981600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:115972600-115976600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:115972600-115977400	Weak transcription	HUVEC	blood vessel
39	chr9:115972600-115978000	Weak transcription	K562	blood
40	chr9:115972600-115980800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:115972600-115981600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:115972600-115981800	Weak transcription	HMEC	breast
43	chr9:115972600-115982800	Weak transcription	Gastric	stomach
44	chr9:115972800-115980800	Weak transcription	Brain Anterior Caudate	brain
45	chr9:115972800-115981000	Weak transcription	Brain Germinal Matrix	brain
46	chr9:115972800-115981800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:115972800-115982000	Weak transcription	HSMMtube	muscle
48	chr9:115973000-115977400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:115973000-115980600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr9:115973000-115980800	Weak transcription	Brain Cingulate Gyrus	brain

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