Variant report

Variant	rs28785294
Chromosome Location	chr2:99823099-99823100
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10496334	1.00[EUR][1000 genomes]
rs10496335	1.00[EUR][1000 genomes]
rs11123760	0.86[EUR][1000 genomes]
rs11123767	1.00[EUR][1000 genomes]
rs11123768	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11526114	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12233087	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12620997	0.86[EUR][1000 genomes]
rs1586434	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1601714	0.91[AMR][1000 genomes]
rs17022249	1.00[EUR][1000 genomes]
rs2091799	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2277876	1.00[EUR][1000 genomes]
rs35071324	1.00[EUR][1000 genomes]
rs3762472	1.00[EUR][1000 genomes]
rs3791211	1.00[EUR][1000 genomes]
rs4851190	0.81[ASN][1000 genomes]
rs56926889	1.00[EUR][1000 genomes]
rs57273701	1.00[EUR][1000 genomes]
rs57743480	1.00[EUR][1000 genomes]
rs58595226	1.00[EUR][1000 genomes]
rs58635701	0.93[EUR][1000 genomes]
rs58745514	1.00[EUR][1000 genomes]
rs59506582	1.00[EUR][1000 genomes]
rs60056452	1.00[EUR][1000 genomes]
rs60653099	1.00[EUR][1000 genomes]
rs6719145	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6746969	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748497	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6749198	0.86[EUR][1000 genomes]
rs7568749	1.00[EUR][1000 genomes]
rs9752510	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
2	chr2:99798800-99825600	Weak transcription	Fetal Heart	heart
3	chr2:99799200-99824200	Weak transcription	Fetal Brain Male	brain
4	chr2:99803800-99829600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:99807000-99832600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:99807600-99825000	Weak transcription	Stomach Mucosa	stomach
7	chr2:99814000-99834800	Weak transcription	Gastric	stomach
8	chr2:99814200-99823600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:99814200-99828200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:99814200-99832400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:99814400-99842200	Weak transcription	Ovary	ovary
12	chr2:99814400-99842800	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:99814800-99840600	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:99815000-99829000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:99815000-99834400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:99815000-99836400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:99815000-99840600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:99815000-99840800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:99815000-99841800	Weak transcription	Pancreas	Pancrea
20	chr2:99815000-99842400	Weak transcription	Fetal Lung	lung
21	chr2:99815200-99827400	Weak transcription	HMEC	breast
22	chr2:99815200-99827600	Weak transcription	Brain Germinal Matrix	brain
23	chr2:99815200-99827600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:99815200-99830400	Weak transcription	Brain Anterior Caudate	brain
25	chr2:99815200-99833200	Weak transcription	Lung	lung
26	chr2:99815200-99838400	Weak transcription	Adipose Nuclei	Adipose
27	chr2:99815200-99840600	Weak transcription	Aorta	Aorta
28	chr2:99815200-99841800	Weak transcription	Spleen	Spleen
29	chr2:99815200-99842000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:99815200-99842400	Weak transcription	Brain Substantia Nigra	brain
31	chr2:99815400-99834400	Weak transcription	NHEK	skin
32	chr2:99815400-99834600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:99815600-99834400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:99815600-99834800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:99815600-99842000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr2:99815600-99842200	Weak transcription	Fetal Stomach	stomach
37	chr2:99815600-99843400	Weak transcription	Fetal Brain Female	brain
38	chr2:99818200-99854600	Weak transcription	Left Ventricle	heart
39	chr2:99818400-99827600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:99818400-99830400	Weak transcription	A549	lung
41	chr2:99818400-99836400	Weak transcription	Brain Angular Gyrus	brain
42	chr2:99818600-99842200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:99818800-99827600	Weak transcription	Primary T cells from cord blood	blood
44	chr2:99818800-99843600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:99819000-99843200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:99822200-99830000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:99822600-99823200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links