Variant report

Variant	rs17046570
Chromosome Location	chr2:55220584-55220585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55216168..55220754-chr2:55221880..55224884,4	MCF-7	breast:
2	chr2:55214294..55216592-chr2:55220369..55222757,2	K562	blood:
3	chr2:55220380..55222677-chr2:55274921..55277767,2	MCF-7	breast:
4	chr2:55219389..55222736-chr2:55233484..55237490,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10170340	0.93[ASN][1000 genomes]
rs10189379	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10496036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs10496037	1.00[CHB][hapmap]
rs12464447	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12464595	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12469804	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12475787	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12475904	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1348528	0.90[CHB][hapmap]
rs17046594	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17347089	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17418675	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]
rs1822618	0.90[CHB][hapmap]
rs2289747	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2864049	0.94[ASN][1000 genomes]
rs55659423	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55698303	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55762835	0.84[ASN][1000 genomes]
rs55993793	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56013263	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6545467	1.00[JPT][hapmap]
rs6707036	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs6713935	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs67156582	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722182	0.82[ASN][1000 genomes]
rs72795431	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72795440	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582359	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7584354	1.00[JPT][hapmap]
rs7584386	1.00[JPT][hapmap]
rs7601625	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs887	0.89[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.90[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:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
3	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
5	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
6	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
7	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
8	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
9	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:55212200-55220600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:55212600-55226400	Weak transcription	Fetal Stomach	stomach
13	chr2:55213800-55226400	Weak transcription	Ovary	ovary
14	chr2:55214200-55224600	Weak transcription	Primary T cells from cord blood	blood
15	chr2:55214200-55225000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:55214400-55222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
19	chr2:55214600-55225600	Weak transcription	NH-A	brain
20	chr2:55214600-55226000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:55214800-55220600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:55214800-55221600	Weak transcription	HSMMtube	muscle
23	chr2:55214800-55221800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr2:55214800-55222000	Weak transcription	GM12878-XiMat	blood
25	chr2:55214800-55223600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:55214800-55223800	Weak transcription	Gastric	stomach
27	chr2:55214800-55224400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:55214800-55224400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:55214800-55224600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:55214800-55225000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr2:55214800-55225000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:55214800-55225200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:55214800-55225200	Weak transcription	Fetal Brain Male	brain
34	chr2:55214800-55225600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:55214800-55225600	Weak transcription	Brain Germinal Matrix	brain
36	chr2:55214800-55226000	Weak transcription	HUVEC	blood vessel
37	chr2:55214800-55226400	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:55214800-55226400	Weak transcription	Fetal Thymus	thymus
39	chr2:55214800-55227200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:55214800-55227200	Weak transcription	HepG2	liver
41	chr2:55214800-55228800	Weak transcription	Fetal Intestine Large	intestine
42	chr2:55214800-55230600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:55214800-55231600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:55214800-55234200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:55214800-55236800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr2:55215000-55222600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:55215000-55225200	Weak transcription	Liver	Liver
48	chr2:55215000-55225800	Weak transcription	Primary B cells from cord blood	blood
49	chr2:55215000-55225800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:55215000-55225800	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links