Variant report

Variant	rs1006459
Chromosome Location	chr20:30064331-30064332
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr20:30063878-30064455	ECC-1	luminal epithelium:	n/a	chr20:30064178-30064195 chr20:30064179-30064196 chr20:30064178-30064194 chr20:30064180-30064196
2	NFIC	chr20:30063739-30065156	SK-N-SH	brain:	n/a	chr20:30064178-30064195 chr20:30064179-30064196 chr20:30064178-30064194 chr20:30064180-30064196

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:30064291-30064341	SK-N-MC	brain:	n/a
2	chr20:30064291-30064341	Jurkat	blood:	n/a
3	chr20:30064291-30064341	GM12891	blood:	n/a
4	chr20:30064291-30064341	A549	lung:	n/a
5	chr20:30064291-30064341	BE2_C	brain:	n/a
6	chr20:30064291-30064341	HepG2	liver:	n/a
7	chr20:30064291-30064341	HAEpiC	amniotic membrane:	n/a
8	chr20:30064291-30064341	ovcar-3	ovarian:	n/a
9	chr20:30064291-30064341	GM06990	blood:	n/a
10	chr20:30064291-30064341	BJ	skin:	n/a
11	chr20:30064291-30064341	AG04449	skin:	fetal
12	chr20:30064291-30064341	CMK	blood:	n/a
13	chr20:30064291-30064341	K562	blood:	n/a
14	chr20:30064291-30064341	SK-N-SH	brain:	n/a
15	chr20:30064291-30064341	SK-N-SH_RA	brain:	n/a
16	chr20:30064291-30064341	AG10803	skin:	n/a
17	chr20:30064291-30064341	LNCaP	prostate:	n/a
18	chr20:30064291-30064341	HPAEpiC	pulmonary alveolar:	n/a
19	chr20:30064291-30064341	MCF10A-Er-Src	breast:	n/a
20	chr20:30064291-30064341	HCF	heart:	n/a
21	chr20:30064291-30064341	PANC-1	pancreas:	n/a
22	chr20:30064291-30064341	HRE	kidney:	n/a
23	chr20:30064291-30064341	H1-hESC	embryonic stem cell:	embryo
24	chr20:30064291-30064341	NHDF-neo	bronchial:	n/a
25	chr20:30064291-30064341	AoSMC	blood vessel:	n/a
26	chr20:30064291-30064341	AG04450	lung:	fetal
27	chr20:30064291-30064341	HCT-116	colon:	n/a
28	chr20:30064291-30064341	SAEC	small airway:	n/a
29	chr20:30064291-30064341	HL-60	blood:	n/a
30	chr20:30064291-30064341	HRPEpiC	eye:	n/a
31	chr20:30064291-30064341	AG09309	skin:	n/a
32	chr20:30064291-30064341	SKMC	muscle:	n/a
33	chr20:30064291-30064341	GM12892	blood:	n/a
34	chr20:30064291-30064341	HEEpiC	esophagus:	n/a
35	chr20:30064291-30064341	Hepatocyte	liver:	n/a
36	chr20:30064291-30064341	Caco-2	colon:	n/a
37	chr20:30064291-30064341	GM19239	blood:	n/a
38	chr20:30064291-30064341	NH-A	brain:	n/a
39	chr20:30064291-30064341	U87	brain:	n/a
40	chr20:30064291-30064341	HCM	heart:	n/a
41	chr20:30064291-30064341	RPTEC	kidney:	n/a
42	chr20:30064291-30064341	PFSK-1	brain:	n/a
43	chr20:30064291-30064341	Hela-S3	cervix:	n/a
44	chr20:30064291-30064341	HIPEpiC	eye:	n/a
45	chr20:30064291-30064341	NB4	blood:	n/a
46	chr20:30064291-30064341	ECC-1	luminal epithelium:	n/a
47	chr20:30064291-30064341	AG09319	gingival:	n/a
48	chr20:30064291-30064341	T-47D	breast:	n/a
49	chr20:30064291-30064341	HUVEC	blood vessel:	n/a
50	chr20:30064291-30064341	HRCEpiC	kidney:	n/a

No data

Variant related genes	Relation type
DEFB124	TF binding region
DEFB124	CpG island

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1543438	0.98[ASN][1000 genomes]
rs2233832	0.81[ASN][1000 genomes]
rs34267307	0.93[ASN][1000 genomes]
rs3761199	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3861819	0.96[ASN][1000 genomes]
rs6057888	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6059425	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6059434	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6059440	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66974934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869384	chr20:29833386-30605088	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
2	nsv470546	chr20:29833609-30235302	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases
3	nsv1055527	chr20:29833958-30078925	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1062069	chr20:29833958-30153486	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv1062612	chr20:29833958-30219337	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
6	nsv1061673	chr20:29833958-30649496	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
7	nsv544232	chr20:29833958-30649496	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
8	nsv1058344	chr20:29835037-30386611	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	402 gene(s)	inside rSNPs	diseases
9	nsv1059672	chr20:29835037-30621271	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
10	esv2763228	chr20:29835049-30239522	Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases
11	nsv949085	chr20:29846303-30473188	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	414 gene(s)	inside rSNPs	diseases
12	nsv1058639	chr20:29877877-30101083	Weak transcription Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv544235	chr20:29877877-30101083	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1058020	chr20:29877877-30197681	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
15	nsv544236	chr20:29877877-30197681	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
16	nsv1063560	chr20:29877877-30435888	Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
17	nsv544237	chr20:29877877-30435888	Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
18	nsv458961	chr20:29893501-30275906	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
19	nsv585911	chr20:29893501-30275906	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
20	nsv1067177	chr20:29900572-30299363	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	383 gene(s)	inside rSNPs	diseases
21	nsv1067419	chr20:30029545-30162261	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
22	nsv544238	chr20:30029545-30162261	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:30062600-30064400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr20:30062600-30064400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
3	chr20:30063200-30064400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
4	chr20:30063200-30064400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
5	chr20:30063200-30064400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
6	chr20:30063600-30064600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr20:30063800-30064400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:30063800-30064400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr20:30063800-30064400	Bivalent Enhancer	Esophagus	oesophagus
10	chr20:30063800-30064800	Bivalent/Poised TSS	Adipose Nuclei	Adipose
11	chr20:30063800-30065200	Bivalent/Poised TSS	Left Ventricle	heart
12	chr20:30063800-30072000	Weak transcription	Pancreas	Pancrea
13	chr20:30063800-30073200	Weak transcription	Ovary	ovary
14	chr20:30064000-30064400	Flanking Active TSS	Fetal Lung	lung
15	chr20:30064000-30064600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
16	chr20:30064000-30064800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
17	chr20:30064000-30065200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr20:30064000-30067200	Weak transcription	Colon Smooth Muscle	Colon
19	chr20:30064000-30071800	Weak transcription	Spleen	Spleen
20	chr20:30064200-30064400	Flanking Active TSS	Lung	lung
21	chr20:30064200-30064400	Bivalent Enhancer	Right Ventricle	heart
22	chr20:30064200-30065400	Weak transcription	Right Atrium	heart

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