Variant report

Variant	rs9828782
Chromosome Location	chr3:99569188-99569189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12330310	1.00[AFR][1000 genomes]
rs13315221	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13320602	1.00[YRI][hapmap]
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]
rs28368726	1.00[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[YRI][hapmap];1.00[AFR][1000 genomes]
rs9810553	1.00[AFR][1000 genomes]
rs9816232	1.00[AFR][1000 genomes]
rs9820799	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9824229	1.00[AFR][1000 genomes]
rs9825382	1.00[AFR][1000 genomes]
rs9825938	1.00[AFR][1000 genomes]
rs9830038	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9831309	1.00[YRI][hapmap]
rs9831706	0.83[AFR][1000 genomes]
rs9833005	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9835048	1.00[YRI][hapmap];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[YRI][hapmap];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[YRI][hapmap];1.00[AFR][1000 genomes]
rs9851985	0.83[AFR][1000 genomes]
rs9852857	1.00[AFR][1000 genomes]
rs9860986	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9862370	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9868303	1.00[AFR][1000 genomes]
rs9870153	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9871500	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9875301	1.00[AFR][1000 genomes]
rs9883235	1.00[YRI][hapmap];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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99557000-99573600	Weak transcription	Small Intestine	intestine
4	chr3:99559000-99578000	Weak transcription	HMEC	breast
5	chr3:99562200-99573200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:99562200-99578000	Weak transcription	NHEK	skin
7	chr3:99562600-99578200	Weak transcription	Fetal Kidney	kidney
8	chr3:99562800-99569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:99562800-99580200	Weak transcription	Gastric	stomach
10	chr3:99563000-99575000	Weak transcription	Placenta	Placenta
11	chr3:99563000-99577600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:99563200-99569200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:99563200-99569400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:99563200-99572200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:99563200-99574800	Weak transcription	Psoas Muscle	Psoas
16	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:99563800-99574800	Weak transcription	Pancreas	Pancrea
18	chr3:99564200-99577600	Weak transcription	Primary B cells from cord blood	blood
19	chr3:99565000-99569400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:99565000-99572000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:99565200-99585000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr3:99565400-99577600	Weak transcription	Fetal Heart	heart
23	chr3:99565600-99569200	Weak transcription	HUVEC	blood vessel
24	chr3:99565600-99569400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr3:99565600-99573600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:99565600-99573600	Weak transcription	Fetal Lung	lung
27	chr3:99565600-99574800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:99565600-99574800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:99565600-99584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:99565600-99589400	Weak transcription	K562	blood
31	chr3:99566000-99571800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:99566000-99571800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:99566000-99572000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:99566000-99573200	Weak transcription	Liver	Liver
35	chr3:99566000-99578400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:99567000-99570000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:99567000-99570200	Strong transcription	HSMM	muscle
38	chr3:99567000-99570400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:99567000-99570800	Strong transcription	Fetal Intestine Large	intestine
40	chr3:99567000-99571600	Strong transcription	NH-A	brain
41	chr3:99567200-99569800	Strong transcription	HSMMtube	muscle
42	chr3:99567200-99570000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:99567200-99570000	Strong transcription	NHLF	lung
44	chr3:99567200-99570800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:99567200-99572000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:99567400-99569400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:99567400-99570400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr3:99567600-99569400	Weak transcription	Lung	lung
49	chr3:99567600-99570000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:99567600-99573600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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