Variant report

Variant	rs10173542
Chromosome Location	chr2:148854049-148854050
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	chr2:148747178..148748066-chr2:148853587..148854325,3	MCF-7	breast:
2	chr2:148852527..148854088-chr2:148860647..148862456,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10171170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10180469	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10191634	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10497028	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10497031	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10803524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10928384	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs1227479	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1227482	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1227484	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234398	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1234399	0.90[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1234400	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1234403	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1234404	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1234414	0.90[JPT][hapmap]
rs1234417	0.83[ASN][1000 genomes]
rs1234420	0.83[ASN][1000 genomes]
rs1234423	0.83[ASN][1000 genomes]
rs1234424	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1234426	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1234427	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1234428	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1234431	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1234432	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12619583	0.83[ASN][1000 genomes]
rs17692648	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs17693310	0.82[ASN][1000 genomes]
rs17743157	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs1994189	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3754541	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs3820715	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs4972323	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4972324	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4972336	0.83[ASN][1000 genomes]
rs59094777	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59984641	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60809905	0.83[ASN][1000 genomes]
rs60850392	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62169531	0.87[ASN][1000 genomes]
rs62169550	0.90[ASN][1000 genomes]
rs62183893	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62183896	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62183921	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62183924	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62183925	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62183933	0.88[EUR][1000 genomes]
rs6430280	0.82[ASN][1000 genomes]
rs6430293	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6430294	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6430301	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6711560	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6714702	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6715654	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6750841	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7571453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7578002	0.83[ASN][1000 genomes]
rs7602932	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1002358	chr2:148703807-148942372	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1007683	chr2:148717347-148942372	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535971	chr2:148717347-148942372	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv869326	chr2:148727068-148859804	Weak transcription Flanking Active TSS Enhancers Strong 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	9 gene(s)	inside rSNPs	diseases
7	nsv817366	chr2:148727068-148879681	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1000852	chr2:148730825-148934986	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv535972	chr2:148730825-148934986	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv916766	chr2:148743880-148955720	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv1014570	chr2:148780080-148869729	Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv535978	chr2:148780080-148869729	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	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
16	nsv535979	chr2:148822091-148859805	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv875276	chr2:148844369-148996824	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148821200-148857600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:148826000-148861000	Weak transcription	Left Ventricle	heart
3	chr2:148834600-148856400	Weak transcription	HSMMtube	muscle
4	chr2:148837600-148866800	Weak transcription	Ovary	ovary
5	chr2:148843600-148860600	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:148845200-148858000	Weak transcription	Aorta	Aorta
7	chr2:148845400-148858000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:148845400-148866000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:148845400-148868000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:148851800-148867600	Weak transcription	Primary T cells from cord blood	blood
11	chr2:148853000-148854200	Enhancers	HUVEC	blood vessel
12	chr2:148853200-148854200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:148853400-148854200	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links