Variant report

Variant	rs10242086
Chromosome Location	chr7:56559173-56559174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUMF2-2	chr7:56558375-56559328	NONHSAT120759

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10215703	0.88[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs10224323	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226486	1.00[ASN][1000 genomes]
rs10226756	1.00[ASN][1000 genomes]
rs10232356	1.00[ASN][1000 genomes]
rs10232838	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10235121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10236798	1.00[ASN][1000 genomes]
rs10237408	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10239401	1.00[ASN][1000 genomes]
rs10247589	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs10259576	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs10266889	1.00[ASN][1000 genomes]
rs10269082	1.00[ASN][1000 genomes]
rs10272852	1.00[ASN][1000 genomes]
rs10281482	1.00[ASN][1000 genomes]
rs10282564	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105304	1.00[ASN][1000 genomes]
rs1105305	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs1105306	1.00[ASN][1000 genomes]
rs11976129	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11977998	1.00[ASN][1000 genomes]
rs12155162	1.00[ASN][1000 genomes]
rs12155169	1.00[ASN][1000 genomes]
rs12534308	1.00[CHD][hapmap]
rs12535550	1.00[CHD][hapmap]
rs12719002	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs12719003	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs13227258	0.92[YRI][hapmap]
rs13231784	1.00[ASN][1000 genomes]
rs13242355	1.00[ASN][1000 genomes]
rs13243299	1.00[ASN][1000 genomes]
rs13245583	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs13307736	1.00[ASN][1000 genomes]
rs13312340	1.00[ASN][1000 genomes]
rs1387067	0.83[CEU][hapmap];0.96[YRI][hapmap];1.00[ASN][1000 genomes]
rs1906629	1.00[ASN][1000 genomes]
rs34614916	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34774343	1.00[ASN][1000 genomes]
rs35043412	1.00[ASN][1000 genomes]
rs3749500	0.88[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs3828495	0.95[CEU][hapmap];0.83[YRI][hapmap]
rs4285439	1.00[ASN][1000 genomes]
rs4442091	1.00[ASN][1000 genomes]
rs56869388	1.00[ASN][1000 genomes]
rs57448144	1.00[ASN][1000 genomes]
rs66831640	1.00[ASN][1000 genomes]
rs67173162	1.00[ASN][1000 genomes]
rs6944931	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952677	1.00[ASN][1000 genomes]
rs6952857	1.00[ASN][1000 genomes]
rs6955935	1.00[ASN][1000 genomes]
rs6957076	1.00[ASN][1000 genomes]
rs6957105	1.00[ASN][1000 genomes]
rs6959032	1.00[ASN][1000 genomes]
rs6968161	1.00[ASN][1000 genomes]
rs6968398	1.00[ASN][1000 genomes]
rs7357108	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs7458882	1.00[ASN][1000 genomes]
rs7782889	1.00[ASN][1000 genomes]
rs7785531	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs7791803	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034712	chr7:56146885-56605592	Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv538861	chr7:56146885-56605592	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv526294	chr7:56171489-56622630	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1016771	chr7:56174828-56643856	Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv538862	chr7:56174828-56643856	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv3368661	chr7:56201127-56591279	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv1033163	chr7:56307057-56677865	ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv538863	chr7:56307057-56677865	ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv888065	chr7:56319050-56580547	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv427783	chr7:56334626-56983646	Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv1022563	chr7:56383876-57318888	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
12	nsv1016255	chr7:56453095-56835595	ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv888066	chr7:56466740-56693762	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1028678	chr7:56511649-56795206	ZNF genes & repeats Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv538864	chr7:56511649-56795206	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv1020833	chr7:56511848-57323499	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
17	nsv538865	chr7:56511848-57323499	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
18	nsv8090	chr7:56511877-56772523	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
19	nsv1017561	chr7:56512618-57334136	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10242086	LANCL2	cis	cerebellum	SCAN
rs10242086	SEPT14	cis	cerebellum	SCAN
rs10242086	CHCHD2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56557600-56561000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
2	chr7:56558600-56564600	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr7:56558800-56564200	ZNF genes & repeats	Duodenum Mucosa	Duodenum

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