Variant report

Variant	rs16994496
Chromosome Location	chr20:14318619-14318620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:14317230-14318799	SK-N-SH	brain:	n/a	n/a
2	JUND	chr20:14318070-14318633	A549	lung:	n/a	chr20:14318317-14318326
3	CTCF	chr20:14318142-14318641	MCF-7	breast:	n/a	n/a
4	SP1	chr20:14317807-14318719	A549	lung:	n/a	n/a
5	RAD21	chr20:14317239-14318963	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr20:14318012-14318755	A549	lung:	n/a	n/a
7	RAD21	chr20:14318100-14318628	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr20:14318153-14318644	HCT-116	colon:	n/a	n/a
9	REST	chr20:14317101-14318713	H1-neurons	neurons:	n/a	n/a
10	MAX	chr20:14317988-14318626	A549	lung:	n/a	n/a
11	CTCF	chr20:14316927-14318891	A549	lung:	n/a	n/a
12	MAX	chr20:14317909-14318640	A549	lung:	n/a	n/a
13	BCL3	chr20:14317682-14318646	A549	lung:	n/a	n/a
14	RAD21	chr20:14318132-14318641	H1-hESC	embryonic stem cell:	n/a	n/a
15	BCL3	chr20:14317905-14318638	A549	lung:	n/a	n/a
16	RAD21	chr20:14318038-14318675	MCF-7	breast:	n/a	n/a
17	RAD21	chr20:14317893-14318796	A549	lung:	n/a	n/a
18	RAD21	chr20:14318145-14318627	GM12878	blood:	n/a	n/a
19	CTCF	chr20:14318540-14318690	GM12872	blood:	n/a	n/a
20	SMC3	chr20:14317037-14318811	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr20:14318027-14318664	MCF-7	breast:	n/a	n/a
22	ATF2	chr20:14318056-14318625	H1-hESC	embryonic stem cell:	n/a	n/a
23	CEBPB	chr20:14318047-14318642	A549	lung:	n/a	n/a
24	TCF12	chr20:14317182-14318750	A549	lung:	n/a	n/a
25	RAD21	chr20:14317386-14318624	IMR90	lung:	n/a	n/a
26	GATA3	chr20:14317836-14318787	A549	lung:	n/a	n/a
27	SMC3	chr20:14318014-14318620	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr20:14318115-14318666	A549	lung:	n/a	n/a
29	RAD21	chr20:14318023-14318716	MCF-7	breast:	n/a	n/a
30	JUND	chr20:14317137-14318735	SK-N-SH	brain:	n/a	chr20:14318317-14318326
31	RAD21	chr20:14318130-14318665	ECC-1	luminal epithelium:	n/a	n/a
32	KAP1	chr20:14317207-14318632	HEK293	kidney:	n/a	n/a
33	CHD1	chr20:14317715-14318658	IMR90	lung:	n/a	n/a
34	CTCF	chr20:14318062-14318680	IMR90	lung:	n/a	n/a
35	RAD21	chr20:14318155-14318628	HepG2	liver:	n/a	n/a
36	EP300	chr20:14317775-14318656	A549	lung:	n/a	n/a
37	RAD21	chr20:14317984-14318766	HCT-116	colon:	n/a	n/a
38	CTCF	chr20:14318079-14318730	HCT-116	colon:	n/a	n/a
39	RAD21	chr20:14318115-14318674	HepG2	liver:	n/a	n/a
40	FOSL2	chr20:14317896-14318668	A549	lung:	n/a	chr20:14318317-14318326

No data

Variant related genes	Relation type
FLRT3	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1114952	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1114953	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1555411	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs16994428	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs16994463	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs16994493	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs16994499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16994501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs1998487	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2208457	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2327820	0.82[ASN][1000 genomes]
rs2876375	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[ASN][1000 genomes]
rs35253731	0.94[ASN][1000 genomes]
rs4814292	0.82[ASN][1000 genomes]
rs55763358	0.82[ASN][1000 genomes]
rs55985306	0.82[ASN][1000 genomes]
rs6033905	0.82[ASN][1000 genomes]
rs6033907	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[ASN][1000 genomes]
rs6033916	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs6033917	0.82[ASN][1000 genomes]
rs6033946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6042601	0.82[ASN][1000 genomes]
rs6042606	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[ASN][1000 genomes]
rs6042614	0.82[ASN][1000 genomes]
rs6042616	0.82[ASN][1000 genomes]
rs6042623	1.00[CHB][hapmap]
rs6042677	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6042678	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6042679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs6074706	0.82[ASN][1000 genomes]
rs6074707	0.82[ASN][1000 genomes]
rs6079359	0.82[ASN][1000 genomes]
rs6079360	0.82[ASN][1000 genomes]
rs6079371	0.82[ASN][1000 genomes]
rs73901234	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8120919	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs912190	0.82[ASN][1000 genomes]
rs9967919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]

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	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1057486	chr20:14077828-14469129	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1066235	chr20:14173771-14389050	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv432101	chr20:14294196-14353346	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv1799128	chr20:14309952-14324140	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14303600-14323400	Weak transcription	Small Intestine	intestine
2	chr20:14313800-14318800	Active TSS	Ovary	ovary
3	chr20:14318400-14318800	Enhancers	Duodenum Smooth Muscle	Duodenum
4	chr20:14318400-14319600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr20:14318400-14320600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr20:14318400-14320600	Weak transcription	Fetal Heart	heart
7	chr20:14318400-14321200	Weak transcription	Fetal Intestine Small	intestine
8	chr20:14318400-14321800	Weak transcription	Fetal Intestine Large	intestine
9	chr20:14318400-14322200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:14318400-14322400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr20:14318400-14322400	Weak transcription	Adipose Nuclei	Adipose
12	chr20:14318400-14322400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr20:14318400-14322600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:14318400-14322600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr20:14318400-14322600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr20:14318400-14322600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:14318400-14322600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr20:14318400-14322600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr20:14318400-14322600	Weak transcription	Psoas Muscle	Psoas
20	chr20:14318400-14322600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr20:14318400-14322600	Weak transcription	Stomach Mucosa	stomach
22	chr20:14318400-14323400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr20:14318400-14325400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr20:14318400-14325600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr20:14318600-14318800	Enhancers	A549	lung
26	chr20:14318600-14322800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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