Variant report

Variant	rs17341838
Chromosome Location	chr3:23261954-23261955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23255785..23258216-chr3:23259980..23262399,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10451986	0.84[ASN][1000 genomes]
rs11129112	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11129114	0.93[ASN][1000 genomes]
rs11916447	0.84[ASN][1000 genomes]
rs11921580	0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs11928344	0.92[ASN][1000 genomes]
rs12185989	1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs12630883	0.87[ASN][1000 genomes]
rs12632777	0.83[ASN][1000 genomes]
rs12633613	0.87[ASN][1000 genomes]
rs12636682	0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1495135	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17343818	0.92[ASN][1000 genomes]
rs17403650	0.92[ASN][1000 genomes]
rs1908772	0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs2172827	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2359637	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359638	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28370926	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2884787	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4368441	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs55895449	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57055494	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57624654	0.92[ASN][1000 genomes]
rs57869672	0.92[ASN][1000 genomes]
rs60407944	0.89[ASN][1000 genomes]
rs6550761	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs6762615	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6764047	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6765562	0.89[ASN][1000 genomes]
rs6766166	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6771053	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771206	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773311	0.89[ASN][1000 genomes]
rs6776770	0.84[ASN][1000 genomes]
rs6778478	0.96[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs6792462	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs6792915	0.83[AFR][1000 genomes]
rs6797467	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6807788	0.96[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs73033545	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033551	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7428484	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7610971	0.92[ASN][1000 genomes]
rs7613733	0.90[ASN][1000 genomes]
rs7613969	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7614926	0.92[ASN][1000 genomes]
rs7622913	0.92[ASN][1000 genomes]
rs7632520	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs7635784	0.87[ASN][1000 genomes]
rs7636536	0.93[ASN][1000 genomes]
rs7638278	0.92[ASN][1000 genomes]
rs7638405	0.92[ASN][1000 genomes]
rs7641764	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs7646505	0.92[ASN][1000 genomes]
rs7649682	0.87[ASN][1000 genomes]
rs7651175	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[ASN][1000 genomes]
rs903518	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9814419	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9820931	0.85[ASN][1000 genomes]
rs9825835	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9835256	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9839409	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9841308	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9841518	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9842014	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9844723	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9845536	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9881808	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9882514	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[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	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23245800-23262800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:23246200-23264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:23246400-23273400	Weak transcription	Aorta	Aorta
4	chr3:23246600-23262400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:23248800-23265800	Weak transcription	Primary T cells from cord blood	blood
6	chr3:23249000-23273400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:23251600-23262800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:23257000-23263200	Enhancers	Brain Hippocampus Middle	brain
9	chr3:23259000-23262200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:23259000-23262600	Enhancers	Colon Smooth Muscle	Colon
11	chr3:23259400-23262400	Enhancers	Liver	Liver
12	chr3:23259600-23262000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:23260400-23262400	Enhancers	Osteobl	bone
14	chr3:23260600-23262400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr3:23260800-23262200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr3:23260800-23262600	Enhancers	Primary B cells from peripheral blood	blood
17	chr3:23260800-23262600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr3:23260800-23270400	Weak transcription	Psoas Muscle	Psoas
19	chr3:23260800-23273400	Weak transcription	Right Atrium	heart
20	chr3:23261000-23262400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:23261000-23262600	Enhancers	Primary B cells from cord blood	blood
22	chr3:23261000-23273400	Weak transcription	Ovary	ovary
23	chr3:23261000-23274400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:23261200-23262400	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:23261200-23262600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:23261200-23264800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:23261200-23272600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:23261400-23262000	Weak transcription	Brain Anterior Caudate	brain
29	chr3:23261400-23262400	Weak transcription	Thymus	Thymus
30	chr3:23261400-23278200	Weak transcription	Brain Angular Gyrus	brain
31	chr3:23261600-23262000	Enhancers	GM12878-XiMat	blood
32	chr3:23261600-23264400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links