Variant report

Variant	rs6964838
Chromosome Location	chr7:3509969-3509970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10215256	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10228151	0.96[CEU][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10232431	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10233166	0.92[CEU][hapmap]
rs10234204	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10235815	0.81[TSI][hapmap]
rs10243467	0.80[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10250421	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap]
rs10250444	0.92[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs10254665	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10256740	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10258501	0.92[CEU][hapmap]
rs10262464	0.91[TSI][hapmap]
rs10266047	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10268837	1.00[CEU][hapmap]
rs10271803	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10274465	0.80[CHD][hapmap]
rs10276933	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs10454314	0.81[TSI][hapmap]
rs10499327	0.88[TSI][hapmap]
rs10807838	0.85[CEU][hapmap]
rs10951155	0.86[JPT][hapmap]
rs1112428	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs11761186	0.81[TSI][hapmap]
rs11771359	0.81[TSI][hapmap]
rs11977306	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs12234397	0.83[CHB][hapmap]
rs12537528	0.82[CEU][hapmap]
rs12700789	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs13221852	0.87[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13237637	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1357309	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs1357310	0.82[CHB][hapmap]
rs1357311	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1403158	0.87[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap]
rs1403162	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1525556	0.92[CEU][hapmap]
rs1554497	0.81[TSI][hapmap]
rs1554498	0.81[TSI][hapmap]
rs1915981	0.82[CHB][hapmap]
rs1915982	0.82[CHB][hapmap]
rs2140114	0.89[TSI][hapmap]
rs2178630	0.83[ASN][1000 genomes]
rs2340848	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2614950	0.86[ASW][hapmap]
rs35153911	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4131987	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs4236326	0.87[TSI][hapmap]
rs4255031	0.82[CEU][hapmap]
rs4316064	0.92[CEU][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs4320450	0.96[CEU][hapmap]
rs4327753	0.89[CEU][hapmap]
rs4443553	0.92[CEU][hapmap]
rs4495320	0.96[CEU][hapmap]
rs4499989	0.82[CEU][hapmap]
rs4506106	0.82[CEU][hapmap]
rs4521670	0.92[CEU][hapmap];0.87[GIH][hapmap];0.96[TSI][hapmap]
rs4544975	0.92[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.98[TSI][hapmap]
rs4607498	0.96[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs4719883	0.83[CEU][hapmap]
rs4719894	0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap]
rs4719944	1.00[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4722663	0.92[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs4722673	0.92[CEU][hapmap]
rs4722693	0.92[CEU][hapmap]
rs4722696	0.81[CEU][hapmap]
rs4722708	0.88[CEU][hapmap]
rs4722827	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4722850	0.82[CHB][hapmap]
rs4722853	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6461994	0.92[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap]
rs6462030	0.89[CEU][hapmap]
rs6462094	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs6462105	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6651070	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6949513	1.00[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6959232	0.96[CEU][hapmap]
rs6962796	0.82[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6965147	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6966619	0.92[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs6974577	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6977110	0.84[YRI][hapmap]
rs7779688	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs7785994	0.92[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap]
rs7789887	0.84[CEU][hapmap]
rs7791343	0.81[TSI][hapmap]
rs7791617	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7797018	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs7798141	0.81[TSI][hapmap]
rs7802250	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7803004	0.96[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes]
rs7803993	0.92[CEU][hapmap]
rs7811244	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs7811286	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs885011	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs9648354	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9969270	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 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	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv869723	chr7:3482682-3566293	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv464270	chr7:3490865-3581357	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv605904	chr7:3490865-3581357	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1027426	chr7:3506255-3556395	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv538672	chr7:3506255-3556395	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6964838	SDK1	cis	lesional skin	skin_eQTL
rs6964838	SDK1	cis	Esophagus Muscularis	GTEx
rs6964838	SDK1	cis	Adipose Subcutaneous	GTEx
rs6964838	SDK1	cis	Muscle Skeletal	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3491200-3526600	Weak transcription	Pancreas	Pancrea
2	chr7:3502000-3521200	Weak transcription	Aorta	Aorta
3	chr7:3504800-3511600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:3506000-3510400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr7:3506200-3521000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:3506400-3510200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:3509200-3510000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:3509200-3510400	Enhancers	Primary T cells from cord blood	blood
9	chr7:3509400-3511400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:3509600-3510000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:3509600-3510600	Weak transcription	Fetal Lung	lung

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