Variant report

Variant	rs10256740
Chromosome Location	chr7:3481667-3481668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10215256	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10224159	0.89[YRI][hapmap]
rs10228151	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10232431	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10233166	0.89[YRI][hapmap]
rs10234204	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10243467	0.99[ASN][1000 genomes]
rs10250421	1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10254665	0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10258501	1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10262783	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs10266047	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10268837	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10270365	1.00[YRI][hapmap]
rs10271803	0.87[ASN][1000 genomes]
rs10274594	0.83[AMR][1000 genomes]
rs10278205	0.88[YRI][hapmap]
rs11974620	0.84[AMR][1000 genomes]
rs12540305	0.85[AMR][1000 genomes]
rs13221852	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13237637	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1357311	0.80[ASN][1000 genomes]
rs1403158	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1403162	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1546742	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1996824	0.92[ASN][1000 genomes]
rs2177167	0.89[YRI][hapmap]
rs2178630	0.89[ASN][1000 genomes]
rs2340848	0.90[ASN][1000 genomes]
rs34608458	0.80[AMR][1000 genomes]
rs35153911	0.82[AMR][1000 genomes]
rs4495320	0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs4521670	0.83[AMR][1000 genomes]
rs4544975	0.83[AMR][1000 genomes]
rs4588749	0.80[AMR][1000 genomes]
rs4607498	0.88[YRI][hapmap];0.80[AMR][1000 genomes]
rs4719894	0.83[AMR][1000 genomes]
rs4719944	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4722693	0.80[AMR][1000 genomes]
rs4722708	0.81[AMR][1000 genomes]
rs4722710	0.84[AMR][1000 genomes]
rs4722712	0.80[AMR][1000 genomes]
rs4722827	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4722853	0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55848061	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55940354	0.81[AMR][1000 genomes]
rs6461994	0.88[YRI][hapmap];0.80[AMR][1000 genomes]
rs6462030	0.84[AMR][1000 genomes]
rs6462040	1.00[YRI][hapmap]
rs6462094	0.90[ASN][1000 genomes]
rs6462105	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6651070	1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6949513	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6959232	0.85[AMR][1000 genomes]
rs6959702	0.80[AMR][1000 genomes]
rs6962796	0.85[ASN][1000 genomes]
rs6964838	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6965147	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6968665	1.00[YRI][hapmap]
rs6969267	0.80[YRI][hapmap]
rs6974075	0.85[AMR][1000 genomes]
rs6974577	0.83[EUR][1000 genomes]
rs7457146	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7790430	0.89[YRI][hapmap]
rs7791617	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7802250	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7803004	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs885011	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9648354	0.88[YRI][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1020764	chr7:3348458-3554820	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv538662	chr7:3348458-3554820	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1030484	chr7:3364990-3506102	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	esv2764026	chr7:3365002-3618361	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1018105	chr7:3365441-3506102	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1026361	chr7:3366960-3502600	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv538664	chr7:3366960-3502600	Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv605893	chr7:3368197-3505231	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1015296	chr7:3381813-3560401	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv1033743	chr7:3395234-3494122	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	nsv1029937	chr7:3408050-3506316	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
18	nsv538668	chr7:3408050-3506316	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	nsv916071	chr7:3423207-3697428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv887329	chr7:3424878-3490865	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv887330	chr7:3424878-3515437	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
22	nsv528715	chr7:3451251-3598581	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv887332	chr7:3455249-3521000	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	nsv605902	chr7:3464896-3598581	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
25	nsv605903	chr7:3472721-3527925	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	nsv887333	chr7:3475716-3542488	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10256740	SDK1	cis	Adipose Subcutaneous	GTEx
rs10256740	SDK1	cis	Muscle Skeletal	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3468800-3482400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:3470400-3482800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:3479400-3484400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:3479600-3492600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:3479800-3483600	Weak transcription	NHEK	skin
6	chr7:3480000-3485600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:3480000-3508600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:3480800-3485200	Weak transcription	HSMM	muscle
9	chr7:3481600-3481800	Enhancers	Left Ventricle	heart

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