Variant report

Variant	rs28368726
Chromosome Location	chr3:99562844-99562845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99562459..99564499-chr3:99581056..99583363,3	MCF-7	breast:
2	chr3:99562547..99565382-chr3:99565632..99567487,2	K562	blood:
3	chr3:99561699..99563246-chr3:99725445..99726435,5	MCF-7	breast:
4	chr3:99562158..99563164-chr3:99972607..99973782,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12330310	1.00[AFR][1000 genomes]
rs13315221	1.00[AFR][1000 genomes]
rs13323384	1.00[AFR][1000 genomes]
rs13327351	0.83[AFR][1000 genomes]
rs13353487	1.00[AFR][1000 genomes]
rs16841800	1.00[AFR][1000 genomes]
rs16841824	1.00[AFR][1000 genomes]
rs16841828	0.83[AFR][1000 genomes]
rs16841836	1.00[AFR][1000 genomes]
rs16846956	0.83[AFR][1000 genomes]
rs28411225	0.83[AFR][1000 genomes]
rs28463921	1.00[AFR][1000 genomes]
rs28508384	1.00[AFR][1000 genomes]
rs28728176	0.83[AFR][1000 genomes]
rs28816814	1.00[AFR][1000 genomes]
rs9809706	1.00[AFR][1000 genomes]
rs9810553	1.00[AFR][1000 genomes]
rs9816232	1.00[AFR][1000 genomes]
rs9820799	1.00[AFR][1000 genomes]
rs9824229	1.00[AFR][1000 genomes]
rs9825382	1.00[AFR][1000 genomes]
rs9825938	1.00[AFR][1000 genomes]
rs9828782	1.00[AFR][1000 genomes]
rs9830038	0.83[AFR][1000 genomes]
rs9831706	0.83[AFR][1000 genomes]
rs9833005	0.83[AFR][1000 genomes]
rs9835048	1.00[AFR][1000 genomes]
rs9837028	1.00[AFR][1000 genomes]
rs9837204	1.00[AFR][1000 genomes]
rs9837555	1.00[AFR][1000 genomes]
rs9841053	1.00[AFR][1000 genomes]
rs9841758	1.00[AFR][1000 genomes]
rs9843919	1.00[AFR][1000 genomes]
rs9844578	1.00[AFR][1000 genomes]
rs9844595	1.00[AFR][1000 genomes]
rs9849336	1.00[AFR][1000 genomes]
rs9849373	1.00[AFR][1000 genomes]
rs9851406	1.00[AFR][1000 genomes]
rs9851985	0.83[AFR][1000 genomes]
rs9852857	1.00[AFR][1000 genomes]
rs9860986	1.00[AFR][1000 genomes]
rs9862370	1.00[AFR][1000 genomes]
rs9868303	1.00[AFR][1000 genomes]
rs9870153	0.83[AFR][1000 genomes]
rs9871500	1.00[AFR][1000 genomes]
rs9875301	1.00[AFR][1000 genomes]
rs9883235	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538000-99563600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
4	chr3:99544200-99564800	Weak transcription	K562	blood
5	chr3:99551200-99566000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:99557000-99573600	Weak transcription	Small Intestine	intestine
7	chr3:99557200-99567200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:99558800-99565000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:99559000-99578000	Weak transcription	HMEC	breast
10	chr3:99561600-99563000	Enhancers	Fetal Intestine Small	intestine
11	chr3:99561600-99563200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:99561600-99563200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:99561600-99563200	Enhancers	Fetal Stomach	stomach
14	chr3:99561600-99563400	Enhancers	HepG2	liver
15	chr3:99561600-99563800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr3:99561600-99563800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:99561600-99564000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:99561600-99564400	Enhancers	Osteobl	bone
19	chr3:99561800-99563200	Enhancers	Fetal Intestine Large	intestine
20	chr3:99561800-99563200	Enhancers	HSMMtube	muscle
21	chr3:99561800-99563200	Enhancers	NH-A	brain
22	chr3:99561800-99563400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:99561800-99563600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:99561800-99563600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:99561800-99563600	Enhancers	Fetal Muscle Leg	muscle
26	chr3:99561800-99563600	Enhancers	NHLF	lung
27	chr3:99561800-99564000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:99561800-99565800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:99561800-99566600	Enhancers	NHDF-Ad	bronchial
30	chr3:99562000-99563000	Enhancers	Liver	Liver
31	chr3:99562000-99563000	Enhancers	Fetal Brain Male	brain
32	chr3:99562000-99563200	Enhancers	Duodenum Mucosa	Duodenum
33	chr3:99562000-99563200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr3:99562000-99563200	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr3:99562000-99563200	Enhancers	Stomach Mucosa	stomach
36	chr3:99562000-99563800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr3:99562000-99563800	Enhancers	Ovary	ovary
38	chr3:99562000-99563800	Enhancers	HSMM	muscle
39	chr3:99562000-99564200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr3:99562000-99565000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:99562000-99565000	Enhancers	Adipose Nuclei	Adipose
42	chr3:99562000-99565600	Enhancers	HUVEC	blood vessel
43	chr3:99562200-99564400	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:99562200-99564800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:99562200-99573200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr3:99562200-99578000	Weak transcription	NHEK	skin
47	chr3:99562400-99563000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:99562400-99563000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:99562400-99563200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:99562400-99563200	Enhancers	Brain Cingulate Gyrus	brain

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