Variant report

Variant	rs13025100
Chromosome Location	chr2:208835700-208835701
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10192065	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10196408	0.92[ASN][1000 genomes]
rs10198217	0.91[ASN][1000 genomes]
rs10221788	0.87[JPT][hapmap]
rs1037416	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10497891	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10497892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10932217	0.82[JPT][hapmap]
rs10932218	0.93[ASN][1000 genomes]
rs10932228	0.80[CEU][hapmap]
rs11674933	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11676872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11679492	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11687058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11687255	0.82[AMR][1000 genomes]
rs11692908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12694097	0.96[ASN][1000 genomes]
rs13006024	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs13011597	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13018735	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13402422	0.95[JPT][hapmap]
rs1466186	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17640827	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1812697	0.90[ASN][1000 genomes]
rs2044971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2100349	0.98[ASN][1000 genomes]
rs2100351	0.98[ASN][1000 genomes]
rs2123294	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2123295	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362782	0.91[ASN][1000 genomes]
rs2362783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34329895	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35086013	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35687108	0.91[ASN][1000 genomes]
rs35726860	0.98[ASN][1000 genomes]
rs35735821	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3795911	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3795912	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4021953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4441448	0.97[ASN][1000 genomes]
rs4507086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4673377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs55883450	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61116354	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62190860	0.83[AMR][1000 genomes]
rs62190895	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6435401	0.86[JPT][hapmap]
rs6711259	0.87[JPT][hapmap]
rs6712527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6718363	0.95[ASN][1000 genomes]
rs6730216	0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6731479	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733857	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6741366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7355275	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7424035	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7562306	0.97[ASN][1000 genomes]
rs7570588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7593972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7595734	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7595823	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7609209	0.90[ASN][1000 genomes]
rs896636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs930746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9679132	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208810400-208841000	Weak transcription	Fetal Lung	lung
2	chr2:208815400-208840800	Weak transcription	Ovary	ovary
3	chr2:208825200-208841400	Weak transcription	Aorta	Aorta
4	chr2:208825600-208841400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:208826600-208841400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:208826800-208840800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:208827200-208841400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:208827200-208841400	Weak transcription	Pancreas	Pancrea
9	chr2:208827400-208841400	Weak transcription	Left Ventricle	heart
10	chr2:208827400-208841400	Weak transcription	Lung	lung
11	chr2:208827400-208857400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:208827800-208840800	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:208828000-208840800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:208828000-208841000	Weak transcription	Fetal Thymus	thymus
15	chr2:208828200-208838600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:208828200-208838600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:208828200-208840400	Weak transcription	Thymus	Thymus
18	chr2:208828200-208841400	Weak transcription	Dnd41	blood
19	chr2:208831800-208836000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:208832000-208836800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr2:208832600-208835800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:208832600-208836200	Enhancers	Duodenum Mucosa	Duodenum
23	chr2:208832800-208836200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:208832800-208841400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:208833400-208836800	Enhancers	Fetal Intestine Small	intestine
26	chr2:208833600-208835800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr2:208834000-208835800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:208834000-208836000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr2:208834000-208836000	Enhancers	HepG2	liver
30	chr2:208834000-208836800	Enhancers	Brain Cingulate Gyrus	brain
31	chr2:208834000-208842600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:208834000-208864000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:208834200-208835800	Enhancers	A549	lung
34	chr2:208834200-208836000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
35	chr2:208834200-208836000	Enhancers	Brain Anterior Caudate	brain
36	chr2:208834200-208836200	Enhancers	Fetal Intestine Large	intestine
37	chr2:208834400-208835800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr2:208834400-208835800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr2:208834400-208836000	Enhancers	Brain Germinal Matrix	brain
40	chr2:208834600-208835800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:208834600-208836000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:208834600-208836000	Enhancers	Brain Hippocampus Middle	brain
43	chr2:208834800-208835800	Enhancers	Primary B cells from peripheral blood	blood
44	chr2:208834800-208835800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:208834800-208836000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr2:208834800-208836000	Enhancers	Psoas Muscle	Psoas
47	chr2:208834800-208836000	Enhancers	Rectal Smooth Muscle	rectum
48	chr2:208834800-208836200	Enhancers	Brain Substantia Nigra	brain
49	chr2:208834800-208865000	Weak transcription	HSMMtube	muscle
50	chr2:208835000-208835800	Enhancers	Colonic Mucosa	Colon

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