Variant report

Variant	rs3990408
Chromosome Location	chr13:49880471-49880472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49879463..49882852-chr13:49885235..49888235,4	MCF-7	breast:
2	chr13:49879461..49882243-chr13:49883363..49884932,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1983806	0.89[JPT][hapmap]
rs60882749	0.91[ASN][1000 genomes]
rs6561498	0.89[JPT][hapmap]
rs6561516	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7321706	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs74074564	0.91[ASN][1000 genomes]
rs7999767	0.90[JPT][hapmap]
rs912547	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9535195	1.00[AFR][1000 genomes]
rs9535196	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49854000-49883000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:49867200-49884200	Weak transcription	Fetal Brain Female	brain
3	chr13:49869600-49882200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:49875800-49881400	Weak transcription	Fetal Lung	lung
5	chr13:49875800-49883800	Weak transcription	Fetal Intestine Small	intestine
6	chr13:49875800-49884000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr13:49875800-49884200	Weak transcription	Primary T cells from cord blood	blood
8	chr13:49875800-49887800	Weak transcription	Fetal Intestine Large	intestine
9	chr13:49875800-49887800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr13:49875800-49891000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr13:49876000-49881400	Weak transcription	Stomach Mucosa	stomach
12	chr13:49876000-49881600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr13:49876000-49882200	Weak transcription	Placenta	Placenta
14	chr13:49876000-49884000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr13:49876200-49884200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr13:49876200-49884200	Weak transcription	Brain Germinal Matrix	brain
17	chr13:49876200-49895000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr13:49876200-49935600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr13:49876400-49887800	Weak transcription	Colonic Mucosa	Colon
20	chr13:49876400-49887800	Weak transcription	Fetal Heart	heart
21	chr13:49876400-49887800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr13:49877200-49883800	Enhancers	Adipose Nuclei	Adipose
23	chr13:49877800-49880600	Enhancers	Esophagus	oesophagus
24	chr13:49877800-49881400	Weak transcription	Fetal Stomach	stomach
25	chr13:49878000-49881600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr13:49878000-49882600	Weak transcription	Fetal Thymus	thymus
27	chr13:49878200-49880800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:49878200-49881600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr13:49878200-49881600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr13:49878200-49881600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:49878200-49881600	Weak transcription	NHLF	lung
32	chr13:49878200-49881600	Weak transcription	Osteobl	bone
33	chr13:49878200-49882200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr13:49878200-49882200	Weak transcription	Liver	Liver
35	chr13:49878200-49882200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr13:49878200-49882400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr13:49878200-49882400	Weak transcription	NH-A	brain
38	chr13:49878200-49893600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr13:49878200-49894800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:49878400-49880600	Weak transcription	Brain Hippocampus Middle	brain
41	chr13:49878400-49881600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr13:49878400-49881600	Weak transcription	Brain Substantia Nigra	brain
43	chr13:49878400-49881600	Weak transcription	Psoas Muscle	Psoas
44	chr13:49878400-49881600	Weak transcription	HSMMtube	muscle
45	chr13:49878400-49881800	Weak transcription	HSMM	muscle
46	chr13:49878400-49882200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr13:49878400-49882400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr13:49878400-49882400	Weak transcription	HUVEC	blood vessel
49	chr13:49878400-49882600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:49878400-49882600	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links