Variant report

Variant	rs3775225
Chromosome Location	chr4:87995613-87995614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87991629..87993752-chr4:87994519..87997259,3	K562	blood:
2	chr4:87856199..87857891-chr4:87995074..87997725,3	MCF-7	breast:
3	chr4:87880122..87883120-chr4:87994863..87997796,2	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction
ENSG00000163633	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10018897	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10516789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1841265	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs19026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236674	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236678	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs236685	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236687	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869642	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2926512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3116679	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342436	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342458	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs342459	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs342460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342461	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs342462	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs342465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3822042	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs384059	0.93[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs390604	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs393991	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs411365	0.91[ASN][1000 genomes]
rs447990	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs60757751	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6827213	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9992235	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[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	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87982600-87999600	Weak transcription	K562	blood
2	chr4:87990200-87999400	Weak transcription	Gastric	stomach
3	chr4:87990200-87999600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:87990200-88008000	Weak transcription	Spleen	Spleen
5	chr4:87990400-87998400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:87990800-88000200	Weak transcription	Fetal Brain Female	brain
7	chr4:87992000-87996200	Enhancers	Primary hematopoietic stem cells	blood
8	chr4:87993800-87995800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr4:87993800-87995800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:87993800-87995800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:87993800-87995800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:87994000-87995800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr4:87994000-87996200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr4:87994200-87995800	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr4:87994200-87996000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:87994200-87996000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr4:87994200-87996000	Enhancers	Fetal Lung	lung
18	chr4:87994200-87997000	Enhancers	Fetal Heart	heart
19	chr4:87994600-87995800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:87994600-87995800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:87994600-87995800	Enhancers	HSMM	muscle
22	chr4:87994600-87996000	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr4:87994800-87996000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:87995000-87996200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:87995200-87995800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:87995200-87995800	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr4:87995200-87995800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:87995200-87995800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr4:87995200-87995800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr4:87995200-87996000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr4:87995200-87996000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr4:87995200-87996000	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr4:87995200-87996200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr4:87995200-87996200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr4:87995200-87996200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr4:87995200-87996200	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr4:87995200-87996200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr4:87995200-87997200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr4:87995200-87998000	Weak transcription	NHDF-Ad	bronchial
40	chr4:87995200-87998400	Weak transcription	HUVEC	blood vessel
41	chr4:87995200-87999200	Enhancers	Brain Angular Gyrus	brain
42	chr4:87995200-87999200	Weak transcription	Osteobl	bone
43	chr4:87995200-87999400	Weak transcription	Small Intestine	intestine
44	chr4:87995200-87999600	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:87995200-88000000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:87995200-88000200	Weak transcription	NH-A	brain
47	chr4:87995200-88000800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr4:87995200-88009400	Weak transcription	HepG2	liver
49	chr4:87995200-88010600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr4:87995200-88029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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