Variant report

Variant	rs6975541
Chromosome Location	chr7:126512020-126512021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1008260	0.85[JPT][hapmap]
rs10215498	1.00[CHB][hapmap]
rs10215590	1.00[CHB][hapmap]
rs10216287	1.00[CHB][hapmap]
rs10227255	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10229765	0.82[JPT][hapmap]
rs10239010	1.00[CHB][hapmap]
rs10241618	0.85[JPT][hapmap]
rs10252649	1.00[CHB][hapmap]
rs10254445	0.85[JPT][hapmap]
rs10254692	1.00[CHB][hapmap]
rs10257388	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10271146	1.00[CHB][hapmap]
rs10487460	1.00[CHB][hapmap]
rs10954133	1.00[CHB][hapmap]
rs11763603	1.00[CHB][hapmap]
rs11763734	1.00[CHB][hapmap]
rs11765100	1.00[CHB][hapmap]
rs11768413	1.00[CHB][hapmap]
rs11769459	0.85[JPT][hapmap]
rs11769491	0.85[JPT][hapmap]
rs11770578	1.00[CHB][hapmap]
rs12333442	1.00[CHB][hapmap]
rs12333645	1.00[CHB][hapmap]
rs12706742	0.85[JPT][hapmap]
rs12706746	1.00[JPT][hapmap]
rs12706747	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs13222700	1.00[CHB][hapmap]
rs13224779	1.00[CHB][hapmap]
rs13225829	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13226065	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs13236505	1.00[CHB][hapmap]
rs13240076	0.85[JPT][hapmap]
rs13240418	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs13242233	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1361988	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1361998	0.85[JPT][hapmap]
rs1362005	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1419492	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1419508	1.00[CHB][hapmap]
rs1557646	1.00[CHB][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs1592370	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs17619947	1.00[CHB][hapmap]
rs17620189	1.00[CHB][hapmap]
rs17620525	0.85[JPT][hapmap]
rs17626816	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs17627206	0.85[JPT][hapmap]
rs17683174	0.84[JPT][hapmap]
rs17683391	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17684592	0.80[GIH][hapmap];0.82[JPT][hapmap]
rs17693362	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1946109	0.85[JPT][hapmap]
rs1946114	1.00[CHB][hapmap]
rs1946115	1.00[CHB][hapmap]
rs1989849	1.00[JPT][hapmap]
rs1989850	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2023733	0.85[JPT][hapmap]
rs2023734	0.85[JPT][hapmap]
rs2023735	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2106352	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2106353	0.82[JPT][hapmap]
rs2106600	1.00[CHB][hapmap]
rs2106601	1.00[CHB][hapmap]
rs2157753	0.85[ASW][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2157977	1.00[CHB][hapmap]
rs2157978	1.00[CHB][hapmap]
rs2157979	1.00[CHB][hapmap]
rs2214159	1.00[CHB][hapmap]
rs2283071	0.85[JPT][hapmap]
rs2283079	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299508	1.00[CHB][hapmap]
rs2299509	1.00[CHB][hapmap]
rs2299510	1.00[CHB][hapmap]
rs2299511	1.00[CHB][hapmap]
rs2299516	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2299517	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2299518	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2299519	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2299520	0.82[ASN][1000 genomes]
rs2896376	1.00[CHB][hapmap]
rs35351503	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35810597	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4728053	0.85[JPT][hapmap]
rs4728054	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4728055	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4731323	0.85[JPT][hapmap]
rs4731330	0.85[JPT][hapmap]
rs4731331	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs4731332	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6467099	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6951643	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6951771	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6969572	1.00[CHB][hapmap]
rs6976213	0.84[ASN][1000 genomes]
rs7809518	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886179	1.00[CHB][hapmap]
rs929211	0.85[JPT][hapmap]
rs954661	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529300	chr7:125669493-126587858	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1032938	chr7:126067684-126587859	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv539119	chr7:126067684-126587859	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv608376	chr7:126457779-126571077	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv608377	chr7:126478190-126512514	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2758132	chr7:126494789-126677843	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2759562	chr7:126494789-126677843	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv427805	chr7:126494789-126677843	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv971498	chr7:126497328-126519764	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv1849599	chr7:126507755-126557892	Enhancers Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6975541	KCP	cis	parietal	SCAN
rs6975541	GCC1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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