Variant report

Variant	rs2099302
Chromosome Location	chr7:3696854-3696855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10226719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10228744	0.85[JPT][hapmap]
rs10245071	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10250929	1.00[JPT][hapmap]
rs10257937	0.88[ASN][1000 genomes]
rs10264803	1.00[JPT][hapmap]
rs10274012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10485876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951207	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10951255	0.90[MEX][hapmap]
rs10951265	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10951266	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951272	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951273	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763915	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11765058	0.82[ASN][1000 genomes]
rs11766767	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11768609	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs11769660	0.81[ASN][1000 genomes]
rs11770829	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11771990	1.00[ASN][1000 genomes]
rs11773388	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12531560	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533563	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534865	1.00[ASN][1000 genomes]
rs12535021	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12535467	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12536371	1.00[ASN][1000 genomes]
rs12536753	0.85[ASN][1000 genomes]
rs12537047	0.82[EUR][1000 genomes]
rs12537980	1.00[ASN][1000 genomes]
rs12538202	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539289	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12539805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12540148	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12540209	0.94[ASN][1000 genomes]
rs12701005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[ASN][1000 genomes]
rs12701014	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13223065	0.82[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs13223852	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs13239833	0.88[ASN][1000 genomes]
rs13240060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240393	0.97[ASN][1000 genomes]
rs13242531	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247619	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17256676	0.81[CEU][hapmap];0.91[TSI][hapmap]
rs17320730	0.82[CEU][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1864841	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1922016	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2002669	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2033441	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2082360	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341579	0.85[ASN][1000 genomes]
rs2341580	0.85[ASN][1000 genomes]
rs2341584	0.82[JPT][hapmap]
rs2341585	0.82[ASN][1000 genomes]
rs2341586	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2614950	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2614951	0.91[ASN][1000 genomes]
rs2614955	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2614957	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2705604	0.82[ASN][1000 genomes]
rs2705609	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2880085	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2880087	1.00[JPT][hapmap]
rs34024103	0.82[ASN][1000 genomes]
rs34108699	0.88[ASN][1000 genomes]
rs34188874	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263851	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34369020	1.00[ASN][1000 genomes]
rs34703718	0.97[ASN][1000 genomes]
rs34704704	0.82[ASN][1000 genomes]
rs34784806	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34872052	0.82[ASN][1000 genomes]
rs34953429	0.82[ASN][1000 genomes]
rs35453716	0.82[ASN][1000 genomes]
rs35513976	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35635220	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35669868	0.82[ASN][1000 genomes]
rs36005986	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3919653	0.87[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4342491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4719998	1.00[ASN][1000 genomes]
rs4719999	1.00[ASN][1000 genomes]
rs4720001	0.97[ASN][1000 genomes]
rs4722903	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4722976	1.00[ASN][1000 genomes]
rs4722993	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722994	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4722995	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722997	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4723014	0.86[MEX][hapmap]
rs62437874	0.82[ASN][1000 genomes]
rs62437895	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62437901	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440182	0.82[ASN][1000 genomes]
rs6462216	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67062941	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6956079	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974350	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6974872	0.94[ASN][1000 genomes]
rs71527450	0.89[ASN][1000 genomes]
rs73037689	0.82[ASN][1000 genomes]
rs752587	1.00[ASW][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap]
rs7779391	1.00[JPT][hapmap]
rs956393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9648355	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs968775	0.82[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
4	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
5	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
6	nsv830888	chr7:3577214-3776276	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv948390	chr7:3609821-3734421	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1033415	chr7:3616095-3753563	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv538680	chr7:3616095-3753563	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1016930	chr7:3627295-3705057	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv530553	chr7:3629504-3736851	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1016270	chr7:3650882-3753563	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv538681	chr7:3650882-3753563	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv605934	chr7:3687012-3738147	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1024837	chr7:3693237-3753563	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2099302	SDK1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3688400-3703200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr7:3688800-3703200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:3688800-3728400	Weak transcription	Aorta	Aorta
4	chr7:3694400-3705800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:3695800-3699400	Weak transcription	Stomach Mucosa	stomach
6	chr7:3696000-3707800	Weak transcription	Pancreas	Pancrea
7	chr7:3696800-3697200	Enhancers	Fetal Muscle Trunk	muscle
8	chr7:3696800-3697400	Enhancers	Fetal Muscle Leg	muscle
9	chr7:3696800-3697400	Enhancers	HSMM	muscle
10	chr7:3696800-3697600	Enhancers	HSMMtube	muscle

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