Variant report

Variant	rs6042506
Chromosome Location	chr20:1458876-1458877
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr20:1458770-1458970	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr20:1458700-1459721	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr20:1458848-1458951	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr20:1458761-1458961	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr20:1458859-1459649	MCF10A-Er-Src	breast:	n/a	chr20:1459394-1459405 chr20:1459387-1459395
6	FOS	chr20:1458784-1459624	MCF10A-Er-Src	breast:	n/a	chr20:1459394-1459405 chr20:1459387-1459395

No.	Distal block	Cell Line	Cell type
1	chr20:1304948..1307524-chr20:1457412..1459794,2	K562	blood:
2	chr20:1453660..1455951-chr20:1456787..1459781,2	K562	blood:
3	chr20:1457689..1459554-chr20:1461112..1463860,2	K562	blood:

Variant related genes	Relation type
NSFL1C	TF binding region
ENSG00000234684	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11087048	1.00[ASN][1000 genomes]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11697973	1.00[ASN][1000 genomes]
rs11697987	1.00[ASN][1000 genomes]
rs11698000	1.00[ASN][1000 genomes]
rs11699494	1.00[CHB][hapmap]
rs13163	1.00[CHB][hapmap]
rs13433171	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	1.00[CHB][hapmap]
rs16994549	1.00[CHB][hapmap]
rs16995146	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16995228	1.00[ASN][1000 genomes]
rs16995310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16995332	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1883933	1.00[CHB][hapmap]
rs1884390	1.00[CHB][hapmap]
rs2064645	1.00[CHB][hapmap]
rs2064646	1.00[CHB][hapmap];1.00[CHD][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];1.00[CHD][hapmap]
rs33999287	1.00[ASN][1000 genomes]
rs35442028	1.00[ASN][1000 genomes]
rs4536713	1.00[ASN][1000 genomes]
rs45512895	1.00[ASN][1000 genomes]
rs4577347	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4813115	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4814102	1.00[CHB][hapmap]
rs4814391	1.00[CHB][hapmap]
rs56035174	1.00[ASN][1000 genomes]
rs57806058	1.00[ASN][1000 genomes]
rs59377624	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59681252	1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6033660	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033672	1.00[ASN][1000 genomes]
rs6033871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap]
rs6041382	1.00[ASN][1000 genomes]
rs6041689	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6041716	1.00[CHB][hapmap]
rs6041717	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6042000	1.00[ASN][1000 genomes]
rs6042550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6043372	1.00[CHB][hapmap]
rs6043374	1.00[CHB][hapmap]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6105101	1.00[CHB][hapmap]
rs6105437	1.00[CHB][hapmap]
rs6109437	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6109511	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6109522	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109740	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6109784	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109984	1.00[CHB][hapmap]
rs6109989	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6110189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110193	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62187542	1.00[ASN][1000 genomes]
rs62187543	1.00[ASN][1000 genomes]
rs62623705	1.00[ASN][1000 genomes]
rs6514337	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6514364	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs715217	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs7271240	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7274052	1.00[ASN][1000 genomes]
rs73067251	1.00[ASN][1000 genomes]
rs73069188	1.00[ASN][1000 genomes]
rs73076965	1.00[ASN][1000 genomes]
rs73076966	1.00[ASN][1000 genomes]
rs73579382	1.00[ASN][1000 genomes]
rs73581208	1.00[ASN][1000 genomes]
rs747611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8117563	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8117744	1.00[ASN][1000 genomes]
rs8118276	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8119259	1.00[ASN][1000 genomes]
rs912113	1.00[CHB][hapmap]
rs958839	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963867	0.91[LWK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1448200-1459000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr20:1450400-1459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:1450400-1459000	Weak transcription	Lung	lung
4	chr20:1451600-1459000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr20:1452000-1459000	Weak transcription	HUVEC	blood vessel
6	chr20:1452000-1459000	Weak transcription	NH-A	brain
7	chr20:1454200-1460800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:1454400-1459000	Weak transcription	Osteobl	bone
9	chr20:1454400-1460400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr20:1454400-1460600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr20:1454400-1460600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr20:1454800-1459000	Weak transcription	A549	lung
13	chr20:1455600-1461600	Enhancers	Placenta	Placenta
14	chr20:1456000-1459200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr20:1456200-1460400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr20:1457200-1459000	Weak transcription	Esophagus	oesophagus
17	chr20:1457200-1459000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr20:1457400-1460800	Strong transcription	Spleen	Spleen
19	chr20:1458000-1459200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr20:1458000-1459400	Flanking Active TSS	HMEC	breast
21	chr20:1458200-1459600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr20:1458400-1459400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr20:1458600-1459000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr20:1458600-1459400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr20:1458600-1459400	Flanking Active TSS	NHEK	skin
26	chr20:1458800-1459200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr20:1458800-1460000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr20:1458800-1460000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr20:1458800-1460400	Enhancers	Hela-S3	cervix
30	chr20:1458800-1460800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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