Variant report

Variant	rs4690090
Chromosome Location	chr4:3389527-3389528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3294234..3297919-chr4:3387466..3390148,3	MCF-7	breast:
2	chr4:3385272..3387718-chr4:3389014..3391654,3	MCF-7	breast:
3	chr4:3388642..3391528-chr4:3405332..3407484,2	MCF-7	breast:
4	chr4:3388406..3390149-chr4:3442407..3445401,2	MCF-7	breast:
5	chr4:3388256..3390546-chr4:3393263..3395293,2	MCF-7	breast:
6	chr4:3386285..3389665-chr4:3485168..3487566,3	MCF-7	breast:
7	chr4:3356602..3361196-chr4:3388835..3391854,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109758	Chromatin interaction
ENSG00000159788	Chromatin interaction
ENSG00000175920	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12644442	0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs13109976	1.00[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13127597	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs13131192	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13152128	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1320762	0.89[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes]
rs1320763	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1406674	0.86[JPT][hapmap]
rs1406675	0.86[JPT][hapmap]
rs16843157	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16844301	0.94[CEU][hapmap];0.82[CHB][hapmap]
rs16844307	0.94[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes]
rs16844309	0.94[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs1730769	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17797467	0.92[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1894442	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1962767	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3213506	0.89[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs3213507	0.95[CEU][hapmap];0.88[CHB][hapmap]
rs3748036	0.88[AMR][1000 genomes]
rs4690093	0.87[AMR][1000 genomes]
rs58143210	0.85[AMR][1000 genomes]
rs62274930	0.82[AMR][1000 genomes]
rs6446740	0.86[JPT][hapmap]
rs6828057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9790656	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3375400-3389600	Weak transcription	NHLF	lung
2	chr4:3378400-3390400	Weak transcription	Ovary	ovary
3	chr4:3378600-3389600	Weak transcription	Aorta	Aorta
4	chr4:3383200-3389600	Weak transcription	Fetal Brain Female	brain
5	chr4:3386200-3390000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:3386200-3391400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:3386400-3390800	Enhancers	Fetal Lung	lung
8	chr4:3386400-3391200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr4:3386600-3390800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:3386600-3392400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:3386600-3393800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:3386800-3389600	Enhancers	Primary B cells from peripheral blood	blood
13	chr4:3386800-3393600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr4:3386800-3393600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:3386800-3395800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:3387200-3389600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:3387400-3389600	Enhancers	HUVEC	blood vessel
18	chr4:3387400-3389800	Weak transcription	Fetal Intestine Large	intestine
19	chr4:3387600-3389600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:3387600-3390600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr4:3387600-3390600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr4:3387600-3392600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:3387800-3389600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:3387800-3389800	Weak transcription	Primary T cells from cord blood	blood
25	chr4:3387800-3389800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:3387800-3391000	Active TSS	Esophagus	oesophagus
27	chr4:3388000-3390200	Active TSS	HMEC	breast
28	chr4:3388000-3394400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:3388200-3389600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:3388200-3389800	Enhancers	Brain Substantia Nigra	brain
31	chr4:3388400-3389600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:3388400-3390000	Enhancers	Fetal Kidney	kidney
33	chr4:3388400-3391200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr4:3388400-3392000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr4:3388400-3393600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:3388600-3389600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr4:3388600-3389800	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr4:3388600-3390000	Enhancers	Left Ventricle	heart
39	chr4:3388600-3392000	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr4:3388600-3392400	Enhancers	Fetal Muscle Trunk	muscle
41	chr4:3388600-3394400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:3388800-3389600	Enhancers	Primary B cells from cord blood	blood
43	chr4:3388800-3389600	Enhancers	Primary hematopoietic stem cells	blood
44	chr4:3388800-3389600	Enhancers	Colon Smooth Muscle	Colon
45	chr4:3388800-3389600	Active TSS	Stomach Smooth Muscle	stomach
46	chr4:3388800-3389600	Enhancers	NH-A	brain
47	chr4:3388800-3389800	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr4:3388800-3389800	Enhancers	Right Ventricle	heart
49	chr4:3388800-3389800	Enhancers	Thymus	Thymus
50	chr4:3388800-3390000	Enhancers	Gastric	stomach

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