Variant report

Variant	rs4809955
Chromosome Location	chr20:52765349-52765350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:53)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:53 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr20:52720353..52721343-chr20:52765343..52766302,5	MCF-7	breast:
2	chr20:52224532..52225159-chr20:52765348..52766166,2	MCF-7	breast:
3	chr20:52765146..52765883-chr3:61793158..61794130,2	MCF-7	breast:
4	chr20:52739465..52740961-chr20:52765012..52766665,338	MCF-7	breast:
5	chr20:52765013..52767443-chr20:55839272..55842153,3	MCF-7	breast:
6	chr20:52739732..52740989-chr20:52765195..52766259,18	MCF-7	breast:
7	chr17:57921159..57923705-chr20:52764319..52767387,3	MCF-7	breast:
8	chr17:56716690..56718038-chr20:52765233..52766444,54	MCF-7	breast:
9	chr20:52739578..52741059-chr20:52765012..52766367,586	MCF-7	breast:
10	chr1:16161756..16162662-chr20:52765346..52766321,2	Hela-S3	cervix:
11	chr20:52739714..52741315-chr20:52765202..52766341,36	MCF-7	breast:
12	chr20:52748821..52749601-chr20:52765286..52765999,2	MCF-7	breast:
13	chr20:52701441..52702056-chr20:52765306..52765991,2	MCF-7	breast:
14	chr20:52715778..52716806-chr20:52765023..52766341,13	MCF-7	breast:
15	chr20:52224532..52225329-chr20:52765348..52766166,4	MCF-7	breast:
16	chr1:116184607..116186215-chr20:52763883..52765833,2	MCF-7	breast:
17	chr20:52224570..52225410-chr20:52765349..52765883,2	MCF-7	breast:
18	chr20:52720034..52720615-chr20:52765098..52765770,2	MCF-7	breast:
19	chr20:52765344..52766249-chr7:107591882..107592609,3	MCF-7	breast:
20	chr1:178749990..178750895-chr20:52764971..52765894,2	MCF-7	breast:
21	chr20:52739738..52741068-chr20:52764992..52766400,210	MCF-7	breast:
22	chr20:52764971..52766731-chr20:52811022..52812911,766	MCF-7	breast:
23	chr17:58422367..58422932-chr20:52765098..52765896,2	MCF-7	breast:
24	chr20:52739042..52740781-chr20:52765292..52766226,10	MCF-7	breast:
25	chr17:56735238..56739776-chr20:52762796..52768683,6	MCF-7	breast:
26	chr20:52277347..52278945-chr20:52765329..52766278,10	MCF-7	breast:
27	chr20:52726536..52727770-chr20:52765262..52766411,6	MCF-7	breast:
28	chr20:52765258..52766191-chr20:52811713..52812860,8	MCF-7	breast:
29	chr20:52764733..52766360-chr20:52810946..52812641,239	MCF-7	breast:
30	chr20:52743107..52744370-chr20:52765246..52766112,8	MCF-7	breast:
31	chr20:52765274..52766299-chr20:55837767..55838761,6	MCF-7	breast:
32	chr20:52743212..52744202-chr20:52765089..52766236,3	MCF-7	breast:
33	chr20:52765145..52766456-chr20:52811076..52812871,393	MCF-7	breast:
34	chr20:41007695..41010681-chr20:52764867..52766401,2	MCF-7	breast:
35	chr20:52278094..52278874-chr20:52765343..52766265,2	MCF-7	breast:
36	chr20:52743247..52744381-chr20:52765148..52766346,109	MCF-7	breast:
37	chr20:52765262..52766080-chr20:52815919..52816758,2	MCF-7	breast:
38	chr17:56735044..56737972-chr20:52763206..52766874,4	MCF-7	breast:
39	chr20:52765302..52765883-chr3:64476876..64477385,2	MCF-7	breast:
40	chr20:52763448..52765793-chr20:55839476..55841287,2	MCF-7	breast:
41	chr20:52743521..52744231-chr20:52765179..52765934,3	MCF-7	breast:
42	chr17:56716670..56718219-chr20:52765018..52766289,42	MCF-7	breast:
43	chr20:52765346..52766284-chr20:52810960..52812568,13	MCF-7	breast:
44	chr20:52765300..52766232-chr20:52803775..52804625,4	MCF-7	breast:
45	chr20:52743170..52744431-chr20:52765148..52766346,200	MCF-7	breast:
46	chr17:56716658..56718401-chr20:52765233..52766626,125	MCF-7	breast:
47	chr20:52765302..52766219-chr20:52784081..52784986,2	MCF-7	breast:
48	chr20:52765182..52766890-chr20:52811098..52812679,34	MCF-7	breast:
49	chr20:52715778..52716806-chr20:52765023..52766312,8	MCF-7	breast:
50	chr20:52765064..52766063-chr20:52814244..52815054,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000091136	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000173218	Chromatin interaction
ENSG00000235415	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000179743	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11905401	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11906715	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11907046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11907150	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11907800	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11907836	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16999008	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870967	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1886308	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1977297	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2274131	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4811492	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4811493	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55733210	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56353101	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57016987	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57562389	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57623780	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57865579	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58978141	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59078348	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59684245	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60250398	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6091819	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6091820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097780	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097782	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6097783	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097784	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097785	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097791	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097792	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097794	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6097796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097801	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62214481	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66870448	0.99[ASN][1000 genomes]
rs7263855	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751090	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8114002	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8114105	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8117971	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8118066	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8118441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs873216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv912945	chr20:52746724-52772741	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv912946	chr20:52758416-52772741	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
5	nsv1063981	chr20:52765317-52776613	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2762085	chr20:52765329-52776625	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv586281	chr20:52765349-52771171	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4809955	C20orf107	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52758600-52768800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:52759000-52765400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr20:52762400-52765400	Enhancers	A549	lung
4	chr20:52764800-52766400	Enhancers	HepG2	liver
5	chr20:52764800-52766600	Enhancers	Hela-S3	cervix

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