Variant report

Variant	rs17772309
Chromosome Location	chr2:46997435-46997436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46883840..46884354-chr2:46996727..46997565,2	MCF-7	breast:
2	chr2:46990483..46993440-chr2:46995579..46997950,2	MCF-7	breast:
3	chr2:46991531..46994585-chr2:46996184..46999045,3	K562	blood:
4	chr2:46992530..46995162-chr2:46996184..46999051,3	K562	blood:
5	chr2:46859579..46860115-chr2:46996827..46997682,2	MCF-7	breast:
6	chr2:46946506..46948828-chr2:46997236..46999160,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10495938	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11889273	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11892177	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11892710	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11893159	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11893443	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11893955	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11901688	1.00[ASN][1000 genomes]
rs17035540	0.88[EUR][1000 genomes]
rs17771005	1.00[YRI][hapmap]
rs17821941	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17822668	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17822704	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41320947	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41349351	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41363351	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41370847	0.88[ASN][1000 genomes]
rs41375646	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41379147	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41432848	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41478946	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4575769	0.81[AFR][1000 genomes]
rs62134765	0.84[AFR][1000 genomes]
rs6721999	0.88[ASN][1000 genomes]
rs6731970	1.00[YRI][hapmap]
rs6735101	0.82[YRI][hapmap]
rs6749450	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72802489	0.86[AFR][1000 genomes]
rs7591613	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7606134	1.00[ASN][1000 genomes]
rs9677705	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[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	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv1013079	chr2:46949337-46998417	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46981400-47006800	Weak transcription	Psoas Muscle	Psoas
2	chr2:46984400-46998600	Weak transcription	Fetal Brain Male	brain
3	chr2:46985600-46998600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:46985600-47008200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:46987200-46997800	Weak transcription	Liver	Liver
6	chr2:46987400-46997600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:46987400-46997600	Weak transcription	Fetal Intestine Small	intestine
8	chr2:46987400-47005600	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:46987400-47005600	Weak transcription	Left Ventricle	heart
10	chr2:46987600-47006000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:46992400-47005400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:46993200-46997600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:46995000-46999000	Enhancers	Osteobl	bone
14	chr2:46995200-46999000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:46995800-46997800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:46996000-47005200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:46997000-46997600	Flanking Active TSS	A549	lung
18	chr2:46997000-46998200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:46997000-46998200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:46997000-46998200	Enhancers	Fetal Lung	lung
21	chr2:46997000-46998400	Enhancers	NHLF	lung
22	chr2:46997000-46999000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:46997200-46997600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:46997200-46997800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr2:46997200-46997800	Enhancers	Ovary	ovary
26	chr2:46997200-46998000	Enhancers	HSMM	muscle
27	chr2:46997200-46998200	Enhancers	NH-A	brain
28	chr2:46997400-46998000	Enhancers	Fetal Intestine Large	intestine
29	chr2:46997400-46998200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:46997400-46998200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:46997400-46998200	Enhancers	Fetal Stomach	stomach
32	chr2:46997400-46998200	Flanking Active TSS	HepG2	liver
33	chr2:46997400-46998800	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links