Variant report

Variant	rs17274896
Chromosome Location	chr2:149001029-149001030
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:148995742..148998637-chr2:149000873..149004003,3	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10206569	0.86[ASN][1000 genomes]
rs10210377	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10432369	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10928388	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10928389	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10928390	0.86[ASN][1000 genomes]
rs1120671	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11675979	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11676308	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678688	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11683219	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11685302	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11692246	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053104	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12470061	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12691780	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12691781	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13001946	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13022005	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13027785	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13032996	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13392141	0.86[ASN][1000 genomes]
rs13425594	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449960	0.91[EUR][1000 genomes]
rs1453318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17276501	0.81[EUR][1000 genomes]
rs1869341	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2044760	0.91[EUR][1000 genomes]
rs2044761	0.90[EUR][1000 genomes]
rs2084954	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167127	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2602358	0.82[EUR][1000 genomes]
rs2656319	0.82[EUR][1000 genomes]
rs2656320	0.82[EUR][1000 genomes]
rs2656324	0.82[EUR][1000 genomes]
rs2839755	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2890917	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35042809	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35749985	0.84[ASN][1000 genomes]
rs4399670	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4972276	0.92[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4972277	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4972278	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4972338	0.89[EUR][1000 genomes]
rs4972341	0.86[ASN][1000 genomes]
rs4972343	0.80[ASN][1000 genomes]
rs4972347	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4972355	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6430305	0.89[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6721794	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6746932	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570104	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7572948	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949679	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs961207	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs987625	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs987626	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs991554	0.91[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001339	chr2:148755022-149020866	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535977	chr2:148755022-149020866	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1004431	chr2:148859099-149054114	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148984400-149011800	Weak transcription	Gastric	stomach
2	chr2:148984800-149011800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:148985400-149011200	Weak transcription	Pancreas	Pancrea
4	chr2:148986000-149002200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:148986800-149011600	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:148990200-149011400	Weak transcription	Spleen	Spleen
7	chr2:148992600-149009600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:148994200-149002200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:148994800-149016600	Weak transcription	Fetal Brain Male	brain
10	chr2:148995000-149001400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:148995000-149002000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:148995000-149002000	Weak transcription	NHDF-Ad	bronchial
13	chr2:148995000-149019800	Weak transcription	Aorta	Aorta
14	chr2:148995000-149030800	Weak transcription	Left Ventricle	heart
15	chr2:148995200-149011000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:148995200-149011400	Weak transcription	Placenta	Placenta
17	chr2:148995400-149001800	Weak transcription	Osteobl	bone
18	chr2:148995400-149002200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:148995400-149002200	Weak transcription	HSMM	muscle
20	chr2:148995400-149003000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:148995400-149010400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:148995400-149011200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:148995400-149011200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:148995400-149011400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:148995400-149013400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:148995400-149015200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:148995600-149001600	Weak transcription	Liver	Liver
28	chr2:148995600-149008400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:148995800-149002000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:148995800-149010800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr2:148996200-149001800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:148996400-149002200	Weak transcription	Small Intestine	intestine
33	chr2:148996400-149007400	Weak transcription	Primary T cells from cord blood	blood
34	chr2:148996400-149008800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:148996400-149010000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr2:148996400-149011400	Weak transcription	Adipose Nuclei	Adipose
37	chr2:148996400-149030400	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:148997000-149001800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:148997000-149012000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr2:148997400-149002200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:148997400-149008600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr2:148997400-149010400	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:148997400-149011000	Weak transcription	Fetal Kidney	kidney
44	chr2:148997600-149009600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:148997800-149002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:148997800-149011400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:148998600-149011000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:148998800-149009800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:148999400-149001800	Weak transcription	Fetal Thymus	thymus
50	chr2:148999400-149006600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links