Variant report

Variant	rs6839663
Chromosome Location	chr4:172993181-172993182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11930028	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171398	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649406	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106245	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13126082	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13136240	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144252	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13150919	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394859	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1505484	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1505487	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1566947	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566950	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34629867	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56703675	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815499	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662946	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676770	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7677518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690716	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990764	0.93[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:41 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022527	chr4:172547732-173236939	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537357	chr4:172547732-173236939	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1024693	chr4:172609237-173236939	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv498033	chr4:172830955-173121438	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv830152	chr4:172906364-173087067	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv596198	chr4:172914759-173035260	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv596199	chr4:172922257-173035260	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv596200	chr4:172932137-173035260	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv881219	chr4:172946287-173024088	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	nsv4605	chr4:172965232-173013447	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
11	nsv508332	chr4:172985686-173001771	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
12	nsv819440	chr4:172986626-172993430	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
13	esv3464622	chr4:172986677-172994875	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
14	esv2607011	chr4:172987211-172993505	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
15	nsv1019420	chr4:172987381-173002876	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
16	esv3489515	chr4:172987477-172994025	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
17	esv3489521	chr4:172987534-172993675	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
18	esv2421911	chr4:172987736-172993181	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
19	nsv964345	chr4:172987752-172994798	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
20	esv2763839	chr4:172987827-172996893	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
21	nsv10611	chr4:172987853-172993423	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
22	esv3464625	chr4:172987902-172994250	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
23	esv3489514	chr4:172987927-172993950	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
24	nsv436418	chr4:172988137-172993369	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
25	esv2565726	chr4:172988187-172993720	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
26	esv3464621	chr4:172988228-172993225	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
27	nsv596204	chr4:172988860-173000808	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
28	esv1816757	chr4:172988860-173001831	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
29	esv1820241	chr4:172988860-173001831	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
30	esv1836240	chr4:172988860-173001831	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
31	esv1836514	chr4:172988860-173001831	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
32	esv1851636	chr4:172988860-173001831	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
33	esv1803044	chr4:172989075-172997356	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
34	esv1803259	chr4:172989075-172997356	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
35	nsv1020025	chr4:172989136-173002876	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
36	nsv1020562	chr4:172989136-173003798	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
37	nsv1024249	chr4:172989136-173005057	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
38	nsv1024492	chr4:172989136-173007548	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
39	esv2760891	chr4:172989148-172997509	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
40	nsv596207	chr4:172989620-173001831	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
41	esv33022	chr4:172990454-172999816	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6839663	MFAP3L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:172992400-172995200	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr4:172992600-172993200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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