Variant report

Variant	rs3739099
Chromosome Location	chr2:47301029-47301030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47295023..47298657-chr2:47300855..47310213,9	MCF-7	breast:
2	chr2:47299662..47307017-chr2:47401146..47405423,11	MCF-7	breast:
3	chr2:47293721..47296795-chr2:47297396..47301843,4	K562	blood:
4	chr2:47298364..47306534-chr2:47399903..47404660,8	K562	blood:

Variant related genes	Relation type
ENSG00000225187	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17036168	0.81[GIH][hapmap]
rs17036208	0.92[EUR][1000 genomes]
rs2280648	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs4953454	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4953455	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4953456	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs59787338	0.87[AMR][1000 genomes]
rs60395026	0.89[EUR][1000 genomes]
rs61377948	0.87[AMR][1000 genomes]
rs6734192	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs6750227	0.89[EUR][1000 genomes]
rs72875120	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv984437	chr2:47270533-47307361	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv873998	chr2:47273732-47313624	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47291800-47301200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr2:47292600-47302200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:47293000-47301400	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr2:47295000-47301200	Enhancers	Left Ventricle	heart
6	chr2:47295000-47301400	Genic enhancers	Esophagus	oesophagus
7	chr2:47295800-47301200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:47295800-47301200	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr2:47296000-47302000	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr2:47296200-47302200	Genic enhancers	Primary B cells from cord blood	blood
11	chr2:47296800-47301400	Enhancers	Adipose Nuclei	Adipose
12	chr2:47297000-47301400	Enhancers	Fetal Heart	heart
13	chr2:47297000-47303000	Genic enhancers	A549	lung
14	chr2:47297600-47302800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:47297800-47303400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:47297800-47303600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:47298000-47301400	Genic enhancers	Duodenum Mucosa	Duodenum
18	chr2:47298000-47303000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:47298000-47303400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:47298000-47304400	Genic enhancers	Spleen	Spleen
21	chr2:47298200-47301200	Enhancers	HSMMtube	muscle
22	chr2:47298800-47302400	Genic enhancers	Placenta	Placenta
23	chr2:47298800-47302800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:47298800-47303000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:47298800-47303200	Enhancers	Fetal Brain Male	brain
26	chr2:47298800-47305200	Strong transcription	Thymus	Thymus
27	chr2:47299000-47301200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
28	chr2:47299000-47303000	Weak transcription	Hela-S3	cervix
29	chr2:47299000-47303400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:47299200-47301200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr2:47299200-47301800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:47299200-47304800	Strong transcription	Primary T cells from cord blood	blood
33	chr2:47299200-47306000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:47299400-47301600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr2:47299400-47301800	Genic enhancers	Colonic Mucosa	Colon
36	chr2:47299400-47302000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:47299400-47302600	Weak transcription	HMEC	breast
38	chr2:47299400-47303800	Genic enhancers	Stomach Smooth Muscle	stomach
39	chr2:47299600-47301600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr2:47299600-47301600	Genic enhancers	Stomach Mucosa	stomach
41	chr2:47299600-47302200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:47299600-47302400	Weak transcription	HUVEC	blood vessel
43	chr2:47299600-47303200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:47299600-47303200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:47299600-47303200	Genic enhancers	Placenta Amnion	Placenta Amnion
46	chr2:47299800-47301600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:47299800-47302600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:47299800-47302600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr2:47299800-47303200	Genic enhancers	Fetal Muscle Leg	muscle
50	chr2:47299800-47303600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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