Variant report

Variant	rs2253693
Chromosome Location	chr20:1545468-1545469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1544908..1546600-chr20:1698607..1700315,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][hapmap]
rs11699494	1.00[CHB][hapmap]
rs16994239	1.00[CHB][hapmap]
rs16994549	1.00[CHB][hapmap]
rs16995146	1.00[CHB][hapmap]
rs16995310	1.00[CHB][hapmap]
rs16995332	1.00[CHB][hapmap]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap]
rs1883933	1.00[CHB][hapmap]
rs1884390	1.00[CHB][hapmap]
rs2064645	1.00[CHB][hapmap]
rs2064646	1.00[CHB][hapmap]
rs2224878	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2249431	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2249832	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.92[MKK][hapmap];0.93[ASN][1000 genomes]
rs2250055	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2250091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MKK][hapmap];0.93[ASN][1000 genomes]
rs2252400	0.84[ASN][1000 genomes]
rs2252401	0.84[ASN][1000 genomes]
rs2252425	0.84[ASN][1000 genomes]
rs2253429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2253431	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2253698	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253815	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2253821	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2255641	0.84[ASN][1000 genomes]
rs2255651	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2255988	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2256095	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2256229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[ASN][1000 genomes]
rs2256240	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2256243	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2256250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[ASN][1000 genomes]
rs2256251	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2263654	0.84[ASN][1000 genomes]
rs2263656	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2263660	0.84[ASN][1000 genomes]
rs2263663	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2422613	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2422614	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2422617	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422618	0.84[ASN][1000 genomes]
rs2873522	1.00[CHB][hapmap]
rs4813115	1.00[CHB][hapmap]
rs4814391	1.00[CHB][hapmap]
rs6033554	1.00[CHB][hapmap]
rs6033660	1.00[CHB][hapmap]
rs6033871	1.00[CHB][hapmap]
rs6033896	1.00[CHB][hapmap]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap]
rs6034039	0.82[MKK][hapmap]
rs6042506	1.00[CHB][hapmap]
rs6042550	1.00[CHB][hapmap]
rs6042568	1.00[CHB][hapmap]
rs6042574	1.00[CHB][hapmap]
rs6042578	1.00[CHB][hapmap]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap]
rs6043372	1.00[CHB][hapmap]
rs6043374	1.00[CHB][hapmap]
rs6074896	1.00[JPT][hapmap]
rs6105031	1.00[CHB][hapmap]
rs6105101	1.00[CHB][hapmap]
rs6105437	1.00[CHB][hapmap]
rs6109740	1.00[CHB][hapmap]
rs6109784	1.00[CHB][hapmap]
rs6109984	1.00[CHB][hapmap]
rs6109989	1.00[CHB][hapmap]
rs6110189	1.00[CHB][hapmap]
rs6110193	1.00[CHB][hapmap]
rs6514337	1.00[CHB][hapmap]
rs6514364	1.00[CHB][hapmap]
rs715217	1.00[CHB][hapmap]
rs7264491	1.00[JPT][hapmap]
rs7271240	1.00[CHB][hapmap]
rs747611	1.00[CHB][hapmap]
rs8117563	1.00[CHB][hapmap]
rs8118276	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2758509	chr20:1476781-1679256	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv2758777	chr20:1476781-1679256	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv428374	chr20:1476781-1679256	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1057036	chr20:1493425-1869281	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv912597	chr20:1500506-1877150	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv510779	chr20:1509330-1613962	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv833894	chr20:1519433-1753366	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv1063015	chr20:1531131-1674430	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv531473	chr20:1532476-1864506	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv9775	chr20:1534985-1563660	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv1814180	chr20:1540847-1601747	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	esv1814535	chr20:1541038-1559940	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv1815886	chr20:1541038-1559940	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv1812605	chr20:1544966-1560140	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2253693	C20orf141	cis	parietal	SCAN
rs2253693	DEFB127	cis	cerebellum	SCAN
rs2253693	QTRT1	trans	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1537000-1551600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr20:1543200-1550400	Weak transcription	Thymus	Thymus
3	chr20:1543600-1548600	Genic enhancers	Primary monocytes fromperipheralblood	blood
4	chr20:1543800-1568000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr20:1544600-1569000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr20:1544800-1548200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr20:1545000-1548000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr20:1545200-1547400	Strong transcription	Primary T cells from cord blood	blood
9	chr20:1545400-1546200	Genic enhancers	Monocytes-CD14+_RO01746	blood
10	chr20:1545400-1546600	Strong transcription	Spleen	Spleen

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