Variant report

Variant	rs1378670
Chromosome Location	chr2:185132244-185132245
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10931121	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12470103	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12470720	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12471114	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12471151	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12472546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476732	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13000012	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13005060	0.99[ASN][1000 genomes]
rs13005737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008457	0.86[ASN][1000 genomes]
rs13010727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13016522	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13018219	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13021358	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1378672	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1526198	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1526211	0.82[ASN][1000 genomes]
rs1534213	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34147693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34311580	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34422167	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34960422	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35628116	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4666968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56112436	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60317026	0.82[EUR][1000 genomes]
rs716544	0.82[ASW][hapmap];1.00[LWK][hapmap]
rs719736	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72904822	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7557221	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:43 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875487	chr2:184737282-185186670	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv998904	chr2:184955270-185318483	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1012174	chr2:184956114-185316664	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv583993	chr2:184995947-185316457	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1002838	chr2:185035277-185289130	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv875490	chr2:185067733-185198135	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv834483	chr2:185082753-185227428	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv818099	chr2:185091908-185134237	Enhancers Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv437303	chr2:185091908-185145099	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv875491	chr2:185091908-185158374	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv875492	chr2:185091908-185198135	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1001745	chr2:185094513-185136906	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1013015	chr2:185094513-185151303	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv2763029	chr2:185094525-185136918	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv2760580	chr2:185094525-185141033	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1009848	chr2:185094537-185136906	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv12193	chr2:185099581-185139440	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv459979	chr2:185099685-185133082	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv583996	chr2:185099685-185133082	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv515830	chr2:185099685-185134237	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv470501	chr2:185099685-185134237	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv583997	chr2:185099685-185134237	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	esv3693447	chr2:185099685-185135444	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	esv2421981	chr2:185099685-185136918	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv1009979	chr2:185100535-185136711	Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv1002832	chr2:185100535-185136759	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv1007348	chr2:185100535-185136806	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv1007571	chr2:185100535-185136906	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv1003172	chr2:185100535-185141033	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv1006174	chr2:185100535-185148412	Weak transcription Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	nsv1006882	chr2:185100535-185154884	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	nsv1007300	chr2:185100535-185185314	Enhancers Active TSS Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
33	nsv1011774	chr2:185100627-185289130	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
34	nsv875494	chr2:185104115-185287387	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
35	nsv997884	chr2:185104678-185136540	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv1001464	chr2:185104678-185136906	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
37	nsv1006661	chr2:185111536-185136906	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
38	nsv1000867	chr2:185111536-185141033	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
39	nsv875495	chr2:185112978-185234102	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
40	nsv998850	chr2:185115342-185136906	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
41	nsv583998	chr2:185118489-185163906	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
42	nsv583999	chr2:185126769-185166472	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
43	nsv438375	chr2:185128121-185134237	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1378670	FSIP2	cis	cerebellum	SCAN
rs1378670	NUP35	cis	parietal	SCAN
rs1378670	NCKAP1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:185127000-185134200	Weak transcription	Adipose Nuclei	Adipose
2	chr2:185129200-185134800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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