Variant report

Variant	rs16994549
Chromosome Location	chr20:1484382-1484383
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:1459193..1460384-chr20:1484138..1484789,4	MCF-7	breast:
2	chr20:1420415..1421693-chr20:1484065..1484901,6	MCF-7	breast:
3	chr20:1455104..1456167-chr20:1483834..1485085,9	MCF-7	breast:
4	chr20:1450508..1451201-chr20:1483798..1484780,3	MCF-7	breast:
5	chr20:1484085..1484840-chr20:1617080..1618039,2	MCF-7	breast:
6	chr20:1418412..1420201-chr20:1482742..1485316,2	K562	blood:
7	chr20:1469550..1472466-chr20:1483678..1485476,2	K562	blood:
8	chr20:1190167..1190684-chr20:1484004..1484618,2	MCF-7	breast:
9	chr20:1294272..1294825-chr20:1484072..1484878,2	MCF-7	breast:
10	chr20:1404065..1404923-chr20:1483919..1484896,2	K562	blood:
11	chr20:1484052..1484617-chr20:1714858..1715446,2	MCF-7	breast:
12	chr20:1407808..1408337-chr20:1484352..1484862,2	MCF-7	breast:
13	chr20:1293822..1294756-chr20:1484015..1484976,4	K562	blood:
14	chr20:1293995..1294735-chr20:1483999..1484561,2	MCF-7	breast:
15	chr20:1455226..1456302-chr20:1484020..1485065,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000125775	Chromatin interaction
ENSG00000196209	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap]
rs11697322	1.00[CEU][hapmap];1.00[CHB][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]
rs11697395	1.00[CHB][hapmap]
rs11699494	1.00[CEU][hapmap];1.00[CHB][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]
rs13163	1.00[CHB][hapmap]
rs16994239	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	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883936	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	1.00[CHB][hapmap]
rs2064645	1.00[CHB][hapmap]
rs2064646	1.00[CHB][hapmap]
rs2249832	1.00[CHB][hapmap]
rs2250091	1.00[CHB][hapmap]
rs2253429	1.00[CHB][hapmap]
rs2253431	1.00[CHB][hapmap]
rs2253693	1.00[CHB][hapmap]
rs2253698	1.00[CHB][hapmap]
rs2256095	1.00[CHB][hapmap]
rs2256229	1.00[CHB][hapmap]
rs2256240	1.00[CHB][hapmap]
rs2256243	1.00[CHB][hapmap]
rs2256250	1.00[CHB][hapmap]
rs2256251	1.00[CHB][hapmap]
rs2263656	1.00[CHB][hapmap]
rs2873522	1.00[CHB][hapmap]
rs4577347	1.00[CHB][hapmap]
rs4813115	1.00[CHB][hapmap]
rs4814102	1.00[CHB][hapmap]
rs4814391	1.00[CHB][hapmap]
rs57094926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap]
rs6033554	1.00[CHB][hapmap]
rs6033660	1.00[CHB][hapmap]
rs6033871	1.00[CHB][hapmap]
rs6033896	1.00[CHB][hapmap]
rs6033911	1.00[ASN][1000 genomes]
rs6033914	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033918	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs6033923	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033935	1.00[CHB][hapmap];0.89[AFR][1000 genomes]
rs6033936	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6041689	1.00[CHB][hapmap]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][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	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs6042588	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042647	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042676	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042682	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6043372	1.00[CHB][hapmap]
rs6043374	1.00[CHB][hapmap]
rs60645920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap]
rs6105101	1.00[CHB][hapmap]
rs6105437	1.00[CHB][hapmap]
rs6109437	1.00[CHB][hapmap]
rs6109511	1.00[CHB][hapmap]
rs6109522	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]
rs66715055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7271240	1.00[CHB][hapmap]
rs747611	1.00[CHB][hapmap]
rs8117563	1.00[CHB][hapmap]
rs8117719	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8118276	1.00[CHB][hapmap]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1481000-1486000	Weak transcription	Hela-S3	cervix
2	chr20:1482000-1497600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr20:1482200-1485600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:1483800-1484800	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr20:1484000-1484800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr20:1484000-1486400	Enhancers	NHEK	skin
7	chr20:1484200-1484400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr20:1484200-1484400	Enhancers	Brain Anterior Caudate	brain
9	chr20:1484200-1484400	Enhancers	Thymus	Thymus
10	chr20:1484200-1484400	Flanking Active TSS	Dnd41	blood
11	chr20:1484200-1484600	Enhancers	Brain Hippocampus Middle	brain
12	chr20:1484200-1484600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr20:1484200-1484800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr20:1484200-1484800	Enhancers	Primary B cells from cord blood	blood
15	chr20:1484200-1484800	Enhancers	Primary B cells from peripheral blood	blood
16	chr20:1484200-1484800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr20:1484200-1484800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr20:1484200-1484800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr20:1484200-1484800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr20:1484200-1484800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr20:1484200-1484800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr20:1484200-1484800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr20:1484200-1484800	Enhancers	Brain Angular Gyrus	brain
24	chr20:1484200-1484800	Enhancers	Brain Substantia Nigra	brain
25	chr20:1484200-1484800	Enhancers	A549	lung
26	chr20:1484200-1484800	Bivalent Enhancer	HUVEC	blood vessel
27	chr20:1484200-1485000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr20:1484200-1488600	Enhancers	HMEC	breast
29	chr20:1484200-1489200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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