Variant report

Variant	rs6949513
Chromosome Location	chr7:3496731-3496732
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10215256	0.92[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10228151	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10232431	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10233166	0.92[CEU][hapmap]
rs10234204	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10235815	0.81[TSI][hapmap]
rs10243467	0.80[CEU][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10250421	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10250444	0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs10254665	0.92[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10256740	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10258501	0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10262464	0.91[TSI][hapmap]
rs10266047	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10268837	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10271803	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs10274465	0.81[CHD][hapmap]
rs10276933	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs10454314	0.81[TSI][hapmap]
rs10499327	0.88[TSI][hapmap]
rs10807838	0.85[CEU][hapmap]
rs10951155	0.87[JPT][hapmap]
rs1112428	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs11761186	0.81[TSI][hapmap]
rs11771359	0.81[TSI][hapmap]
rs12537528	0.82[CEU][hapmap]
rs12540305	0.80[AMR][1000 genomes]
rs12700789	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs13221852	0.96[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13237637	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1357311	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1403158	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1403162	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1525556	0.92[CEU][hapmap]
rs1546742	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1554497	0.81[TSI][hapmap]
rs1554498	0.81[TSI][hapmap]
rs1996824	0.80[ASN][1000 genomes]
rs2140114	0.89[TSI][hapmap]
rs2178630	0.93[ASN][1000 genomes]
rs2340848	0.85[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs35153911	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4131987	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4236326	0.87[TSI][hapmap]
rs4255031	0.82[CEU][hapmap]
rs4316064	0.92[CEU][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs4320450	0.96[CEU][hapmap];0.86[CHB][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];0.98[GIH][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap]
rs4544975	0.92[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs4607498	0.96[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs4719883	0.83[CEU][hapmap]
rs4719894	0.92[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap]
rs4719944	0.90[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4722663	0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][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	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4722853	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55848061	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6461994	0.92[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap]
rs6462030	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6462094	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs6462105	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6651070	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6959232	0.96[CEU][hapmap];0.80[AMR][1000 genomes]
rs6962796	0.82[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6964838	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]
rs6965147	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6966619	0.92[CEU][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs6974075	0.80[AMR][1000 genomes]
rs6974577	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7457146	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7785994	0.92[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs7789887	0.84[CEU][hapmap]
rs7791343	0.81[TSI][hapmap]
rs7791617	1.00[CEU][hapmap];0.83[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7797018	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs7798141	0.81[TSI][hapmap]
rs7802250	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7803004	0.96[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7803993	0.92[CEU][hapmap]
rs7811244	0.92[CEU][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs7811286	0.85[CEU][hapmap];0.87[JPT][hapmap]
rs885011	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9648354	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9969270	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 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	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	nsv1026295	chr7:3485871-3505092	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
27	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
28	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6949513	SDK1	cis	Adipose Subcutaneous	GTEx
rs6949513	C7orf50	cis	parietal	SCAN
rs6949513	MAD1L1	cis	parietal	SCAN
rs6949513	SDK1	cis	Muscle Skeletal	GTEx
rs6949513	C7orf27	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3480000-3508600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr7:3491200-3526600	Weak transcription	Pancreas	Pancrea
3	chr7:3493600-3506000	Weak transcription	HSMM	muscle
4	chr7:3494400-3497400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:3495000-3497000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:3495600-3496800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr7:3496000-3507000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:3496200-3497000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr7:3496400-3497000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:3496400-3497000	ZNF genes & repeats	Aorta	Aorta
11	chr7:3496400-3497000	Enhancers	Placenta Amnion	Placenta Amnion
12	chr7:3496600-3503200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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