Variant report

Variant	rs17418675
Chromosome Location	chr2:55210605-55210606
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10170340	0.83[ASN][1000 genomes]
rs10189379	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10496036	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10496037	0.81[CHB][hapmap]
rs12464447	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12464595	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12469804	0.81[CHB][hapmap]
rs12475787	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12475904	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12479297	0.83[ASN][1000 genomes]
rs17046570	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17046594	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17347089	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2289747	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2864049	0.85[ASN][1000 genomes]
rs55659423	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55698303	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55993793	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56013263	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545467	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6707036	0.85[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs6713935	0.81[CHB][hapmap]
rs67156582	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6730728	0.83[ASN][1000 genomes]
rs72795431	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72795440	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7582359	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7584354	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7584386	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7601625	1.00[JPT][hapmap]
rs887	0.94[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55193400-55214800	Strong transcription	HepG2	liver
5	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:55195000-55215200	Strong transcription	Dnd41	blood
9	chr2:55195600-55210800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:55196200-55214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
13	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:55198200-55212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:55198600-55215200	Weak transcription	Lung	lung
18	chr2:55198800-55215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:55199200-55212400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:55200400-55213400	Weak transcription	Fetal Brain Male	brain
21	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
22	chr2:55203800-55210800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
24	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
25	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
26	chr2:55204200-55214800	Strong transcription	Fetal Thymus	thymus
27	chr2:55204800-55211600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:55205000-55211600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:55205200-55213400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:55205200-55213600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:55205200-55214600	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:55205200-55214600	Weak transcription	Right Atrium	heart
33	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
34	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
35	chr2:55205600-55211000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:55205600-55214800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:55205800-55211800	Weak transcription	Fetal Stomach	stomach
38	chr2:55205800-55216000	Weak transcription	Fetal Intestine Small	intestine
39	chr2:55206200-55213000	Enhancers	Brain Cingulate Gyrus	brain
40	chr2:55206400-55214800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:55206600-55214000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:55206600-55214800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:55206600-55215200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:55206800-55213800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:55206800-55214800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:55207000-55210800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:55207200-55212800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:55207200-55213200	Weak transcription	Fetal Brain Female	brain
49	chr2:55207600-55211200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:55207600-55214800	Strong transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links