Variant report

Variant	rs9996559
Chromosome Location	chr4:89976734-89976735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:45005434..45006381-chr4:89976624..89977229,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10000140	0.86[AMR][1000 genomes]
rs10024807	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10027874	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10029662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030342	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11097209	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097210	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097211	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507819	0.83[AMR][1000 genomes]
rs13115669	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13140085	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150503	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17014898	0.95[ASN][1000 genomes]
rs17014901	0.95[ASN][1000 genomes]
rs17014988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056012	0.91[AMR][1000 genomes]
rs28379646	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34378169	0.91[ASN][1000 genomes]
rs34693890	0.95[ASN][1000 genomes]
rs36048928	0.95[ASN][1000 genomes]
rs59385067	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61286299	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532102	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67317338	0.95[ASN][1000 genomes]
rs6823660	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6826407	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827398	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853075	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857969	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660377	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668782	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7674344	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874147	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992522	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89944200-89978000	Weak transcription	Pancreas	Pancrea
2	chr4:89973200-89977000	Weak transcription	Psoas Muscle	Psoas
3	chr4:89973400-89976800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:89973400-89977800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:89973400-89977800	Weak transcription	Right Ventricle	heart
6	chr4:89973600-89977800	Weak transcription	Placenta	Placenta
7	chr4:89975200-89976800	Enhancers	Fetal Heart	heart
8	chr4:89975200-89977200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:89975200-89979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:89975400-89977000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:89975400-89977000	Enhancers	Primary hematopoietic stem cells	blood
12	chr4:89975600-89976800	Enhancers	Fetal Intestine Large	intestine
13	chr4:89975600-89977000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr4:89975600-89977000	Weak transcription	Fetal Brain Male	brain
15	chr4:89975600-89977000	Weak transcription	Hela-S3	cervix
16	chr4:89975600-89977800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:89975600-89978400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:89975600-89978800	Active TSS	Duodenum Mucosa	Duodenum
19	chr4:89975800-89976800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:89975800-89976800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr4:89975800-89976800	Enhancers	NH-A	brain
22	chr4:89975800-89977000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:89975800-89977000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr4:89975800-89977000	Enhancers	NHEK	skin
25	chr4:89975800-89977200	Enhancers	Small Intestine	intestine
26	chr4:89975800-89978400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr4:89975800-89978800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:89976000-89976800	Weak transcription	GM12878-XiMat	blood
29	chr4:89976000-89977200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:89976000-89978400	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr4:89976000-89978800	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr4:89976000-89978800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:89976000-89978800	Active TSS	Aorta	Aorta
34	chr4:89976000-89978800	Active TSS	Right Atrium	heart
35	chr4:89976200-89976800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr4:89976200-89976800	Weak transcription	Fetal Muscle Leg	muscle
37	chr4:89976200-89976800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:89976200-89977000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:89976200-89977000	Weak transcription	Fetal Stomach	stomach
40	chr4:89976200-89977000	Weak transcription	Stomach Mucosa	stomach
41	chr4:89976200-89977200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:89976200-89977400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:89976200-89978600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:89976200-89978600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr4:89976200-89978800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:89976200-89978800	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr4:89976200-89978800	Active TSS	Ovary	ovary
48	chr4:89976400-89976800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:89976400-89976800	Flanking Active TSS	Colon Smooth Muscle	Colon
50	chr4:89976400-89976800	Enhancers	Rectal Mucosa Donor 29	rectum

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