Variant report

Variant	rs4409957
Chromosome Location	chr13:96144704-96144705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10219866	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11617639	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11619150	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11843974	0.87[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs12427460	0.87[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs12866697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12872431	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12876693	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12876913	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1570903	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1570904	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890373	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4322517	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4335657	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4351928	0.88[ASN][1000 genomes]
rs4387474	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4394950	0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4402421	0.82[ASN][1000 genomes]
rs4403921	0.86[ASN][1000 genomes]
rs4408415	0.85[ASN][1000 genomes]
rs4466958	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4547209	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4564445	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4564446	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4587819	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4609701	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4771917	0.86[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs4773907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4773908	0.87[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs4773909	0.89[ASN][1000 genomes]
rs4773910	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4773911	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4773912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492792	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492793	0.92[ASN][1000 genomes]
rs6492796	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492797	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492798	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492799	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492807	0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs7139829	0.90[ASN][1000 genomes]
rs7322391	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7326265	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7326546	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7328468	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7332888	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7332917	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7338647	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7489425	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7982486	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7982563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7984234	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7990054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7992297	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7995104	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7995114	0.82[ASN][1000 genomes]
rs7995959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8002444	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8002639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs877960	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs877961	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs877962	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs927786	0.88[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs927787	0.87[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs927788	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs9302074	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9302075	0.87[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs9302076	0.88[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs946228	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs946231	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516589	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516590	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516592	0.84[EUR][1000 genomes]
rs9524982	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524983	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524986	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9524987	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524988	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524989	0.88[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs9524991	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs9561880	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9590285	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9590286	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9590287	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9590288	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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	nsv1043019	chr13:95924585-96152616	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1037673	chr13:95930191-96146554	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541882	chr13:95930191-96146554	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2752652	chr13:96059024-96181597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv900933	chr13:96138087-96215289	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96143800-96145400	Enhancers	Stomach Mucosa	stomach
2	chr13:96144200-96145000	Enhancers	H1 Cell Line	embryonic stem cell
3	chr13:96144200-96145000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:96144200-96145000	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr13:96144200-96145000	Enhancers	HMEC	breast
6	chr13:96144200-96145400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr13:96144400-96145000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:96144600-96145000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr13:96144600-96145000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr13:96144600-96145000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr13:96144600-96145000	Enhancers	Hela-S3	cervix
12	chr13:96144600-96145200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
13	chr13:96144600-96145200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr13:96144600-96145200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:96144600-96145400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr13:96144600-96145600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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