Variant report

Variant	rs12998848
Chromosome Location	chr2:189650206-189650207
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189469579..189472035-chr2:189650010..189652348,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10084412	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10166484	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10209411	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10804023	0.84[EUR][1000 genomes]
rs10804024	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10931381	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10931382	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1157434	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11679794	0.90[EUR][1000 genomes]
rs11686942	0.87[EUR][1000 genomes]
rs11891828	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11901929	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11902285	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12185550	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12470289	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12617610	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12619491	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12620233	0.87[EUR][1000 genomes]
rs12624180	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12624203	0.90[EUR][1000 genomes]
rs12693513	0.84[EUR][1000 genomes]
rs13001931	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13012958	0.81[EUR][1000 genomes]
rs13017203	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13020633	0.91[EUR][1000 genomes]
rs13024524	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13026165	0.90[EUR][1000 genomes]
rs1354907	0.84[EUR][1000 genomes]
rs1395864	0.84[EUR][1000 genomes]
rs1395865	0.84[EUR][1000 genomes]
rs1400946	0.87[EUR][1000 genomes]
rs1507554	0.84[EUR][1000 genomes]
rs1507555	0.83[EUR][1000 genomes]
rs1516448	0.80[EUR][1000 genomes]
rs1516449	1.00[JPT][hapmap]
rs1518006	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1518010	0.88[EUR][1000 genomes]
rs1518011	0.87[EUR][1000 genomes]
rs1518012	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1518013	0.90[EUR][1000 genomes]
rs1518014	0.90[EUR][1000 genomes]
rs1518016	0.84[EUR][1000 genomes]
rs1524375	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1568235	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1589133	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1605462	0.86[CHB][hapmap]
rs1607315	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17355585	1.00[JPT][hapmap]
rs1829305	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1848280	0.84[EUR][1000 genomes]
rs1850553	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1878650	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1995700	0.84[EUR][1000 genomes]
rs1995701	0.84[EUR][1000 genomes]
rs1995702	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1996457	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1996987	0.84[EUR][1000 genomes]
rs2138959	0.89[EUR][1000 genomes]
rs2138960	0.90[EUR][1000 genomes]
rs2176501	0.87[EUR][1000 genomes]
rs2177544	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2351099	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2708209	1.00[JPT][hapmap]
rs34017611	0.90[EUR][1000 genomes]
rs3856335	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4261667	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4306657	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4666764	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667243	0.87[EUR][1000 genomes]
rs4667244	0.86[EUR][1000 genomes]
rs4667245	0.87[EUR][1000 genomes]
rs4667249	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6434294	0.84[EUR][1000 genomes]
rs6710589	0.90[EUR][1000 genomes]
rs6711038	0.90[EUR][1000 genomes]
rs6744781	0.87[EUR][1000 genomes]
rs6748400	0.90[EUR][1000 genomes]
rs6757283	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7583964	0.87[EUR][1000 genomes]
rs7587646	0.90[EUR][1000 genomes]
rs7587851	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7590689	0.91[EUR][1000 genomes]
rs7594142	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7598731	0.90[EUR][1000 genomes]
rs7600697	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs981265	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1000932	chr2:189542210-189677277	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv536088	chr2:189542210-189677277	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875606	chr2:189579045-189688463	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875607	chr2:189579045-189711790	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1008847	chr2:189603961-189769705	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv997454	chr2:189615728-189770133	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1002175	chr2:189615728-189776301	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189646200-189650400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:189646400-189650400	Weak transcription	Fetal Heart	heart
3	chr2:189648400-189650400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:189648400-189650800	Enhancers	Muscle Satellite Cultured Cells	--
5	chr2:189648400-189651200	Enhancers	Osteobl	bone
6	chr2:189648400-189653400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:189648600-189651600	Enhancers	NHDF-Ad	bronchial
8	chr2:189649000-189651400	Weak transcription	A549	lung
9	chr2:189649000-189652800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:189649200-189650400	Weak transcription	HSMM	muscle
11	chr2:189649200-189651200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:189649200-189651200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:189649200-189651200	Weak transcription	HMEC	breast
14	chr2:189649400-189650400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:189649400-189650400	Weak transcription	HSMMtube	muscle
16	chr2:189649400-189650400	Weak transcription	NH-A	brain
17	chr2:189649400-189650800	Weak transcription	NHEK	skin
18	chr2:189649600-189651400	Enhancers	Colon Smooth Muscle	Colon
19	chr2:189649800-189650600	Enhancers	Rectal Smooth Muscle	rectum
20	chr2:189649800-189650600	Enhancers	Stomach Smooth Muscle	stomach
21	chr2:189650000-189650400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:189650000-189651000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:189650000-189651200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr2:189650200-189652000	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links