Variant report

Variant	rs16998585
Chromosome Location	chr20:52556562-52556563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:363)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:363 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr20:52556526-52556772	K562	blood:	n/a	n/a
2	MYC	chr20:52556244-52556723	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr20:52556518-52556739	ProgFib	skin:	n/a	n/a
4	REST	chr20:52556191-52556941	A549	lung:	n/a	n/a
5	RAD21	chr20:52556315-52556838	HepG2	liver:	n/a	n/a
6	TCF12	chr20:52555870-52556981	SK-N-SH	brain:	n/a	n/a
7	CUX1	chr20:52556407-52556808	GM12878	blood:	n/a	n/a
8	CTCF	chr20:52556560-52556710	NB4	blood:	n/a	n/a
9	CTCF	chr20:52556500-52556650	BJ	skin:	n/a	n/a
10	CTCF	chr20:52556540-52556690	GM12871	blood:	n/a	n/a
11	TEAD4	chr20:52556183-52557141	K562	blood:	n/a	n/a
12	CTCF	chr20:52556473-52556727	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr20:52555986-52556865	A549	lung:	n/a	n/a
14	MXI1	chr20:52556427-52556816	GM12878	blood:	n/a	n/a
15	CTCF	chr20:52556540-52556690	AG04450	lung:	n/a	n/a
16	CTCF	chr20:52556560-52556710	HEK293	kidney:	n/a	n/a
17	ZC3H11A	chr20:52556199-52556902	K562	blood:	n/a	n/a
18	FOS	chr20:52556328-52556729	MCF10A-Er-Src	breast:	n/a	n/a
19	CTCF	chr20:52556500-52556752	HepG2	liver:	n/a	n/a
20	CTCF	chr20:52556500-52556650	K562	blood:	n/a	n/a
21	CTCF	chr20:52556520-52556670	GM12866	blood:	n/a	n/a
22	RFX5	chr20:52556358-52556757	K562	blood:	n/a	n/a
23	TBP	chr20:52556299-52556843	HepG2	liver:	n/a	n/a
24	POU2F2	chr20:52556455-52556739	GM12891	blood:	n/a	n/a
25	CTCF	chr20:52556495-52556745	Hela-S3	cervix:	n/a	n/a
26	CEBPB	chr20:52556052-52556884	A549	lung:	n/a	chr20:52556562-52556573
27	CTCF	chr20:52556474-52556760	Medullo	brain:	n/a	n/a
28	TEAD4	chr20:52556511-52556892	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr20:52556540-52556690	AG10803	skin:	n/a	n/a
30	RUNX3	chr20:52556057-52556773	GM12878	blood:	n/a	n/a
31	GATA3	chr20:52556041-52556732	T-47D	breast:	n/a	n/a
32	BATF	chr20:52556455-52556772	GM12878	blood:	n/a	n/a
33	FOXM1	chr20:52556259-52556977	GM12878	blood:	n/a	n/a
34	JUND	chr20:52556161-52556772	K562	blood:	n/a	n/a
35	RAD21	chr20:52556156-52556810	GM12878	blood:	n/a	n/a
36	GATA3	chr20:52556065-52556768	A549	lung:	n/a	n/a
37	EP300	chr20:52555969-52556912	A549	lung:	n/a	n/a
38	CTCF	chr20:52556489-52556738	MCF-7	breast:	n/a	n/a
39	YY1	chr20:52556473-52556872	A549	lung:	n/a	n/a
40	CTCF	chr20:52556560-52556710	WERI-Rb-1	eye:	n/a	n/a
41	MAX	chr20:52555901-52556836	NB4	blood:	n/a	n/a
42	USF2	chr20:52556529-52556694	HepG2	liver:	n/a	n/a
43	RAD21	chr20:52556350-52556761	GM12878	blood:	n/a	n/a
44	EP300	chr20:52556466-52556718	SK-N-SH_RA	brain:	n/a	n/a
45	FOS	chr20:52556159-52556700	MCF10A-Er-Src	breast:	n/a	n/a
46	STAT5A	chr20:52556347-52556809	GM12878	blood:	n/a	n/a
47	CTCF	chr20:52556560-52556710	GM12866	blood:	n/a	n/a
48	CEBPB	chr20:52555853-52556974	H1-hESC	embryonic stem cell:	n/a	chr20:52556562-52556573
49	CTCF	chr20:52556521-52556726	SK-N-SH_RA	brain:	n/a	n/a
50	YY1	chr20:52556465-52557085	GM12892	blood:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52198633..52199695-chr20:52556115..52556780,3	MCF-7	breast:
2	chr17:59474996..59480161-chr20:52556121..52561884,6	MCF-7	breast:
3	chr20:52532023..52532688-chr20:52555703..52556632,2	MCF-7	breast:
4	chr20:49411382..49413304-chr20:52553862..52556702,3	MCF-7	breast:
5	chr17:58145680..58147362-chr20:52554822..52556632,2	MCF-7	breast:
6	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
7	chr17:56706658..56709234-chr20:52552890..52557689,4	MCF-7	breast:
8	chr17:59939253..59942212-chr20:52554185..52557076,2	MCF-7	breast:
9	chr20:52556025..52558052-chr4:57843937..57845567,2	MCF-7	breast:
10	chr17:48157159..48157813-chr20:52556453..52557192,2	MCF-7	breast:
11	chr17:59488616..59494924-chr20:52554630..52559372,9	MCF-7	breast:
12	chr20:52499798..52500636-chr20:52556044..52556576,2	MCF-7	breast:
13	chr20:52554988..52556740-chr20:55798732..55800489,2	MCF-7	breast:
14	chr17:56707751..56710392-chr20:52555190..52558925,4	MCF-7	breast:
15	chr20:52554098..52560340-chr20:52684210..52688448,9	MCF-7	breast:
16	chr20:49347041..49349298-chr20:52555192..52557887,2	MCF-7	breast:
17	chr17:56736212..56737922-chr20:52556344..52558393,2	MCF-7	breast:
18	chr17:59485646..59489353-chr20:52553682..52557868,4	MCF-7	breast:
19	chr20:52556485..52556988-chr20:55818772..55819273,2	MCF-7	breast:
20	chr20:52556047..52557092-chr3:64008811..64009718,4	MCF-7	breast:
21	chr20:52554600..52557238-chr20:55797829..55800165,3	MCF-7	breast:
22	chr20:52553226..52558762-chr20:55837122..55843874,19	MCF-7	breast:
23	chr20:52224289..52226213-chr20:52555088..52557591,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000236352	TF binding region
ENSG00000267131	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000005884	Chromatin interaction
ENSG00000235415	Chromatin interaction
ENSG00000265595	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000163636	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000047315	Chromatin interaction
ENSG00000084092	Chromatin interaction
ENSG00000124243	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs16998583	0.85[TSI][hapmap]

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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
3	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
4	nsv1055549	chr20:52555871-52586281	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16998585	SLC9A8	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52549000-52558800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr20:52550000-52556800	Enhancers	Primary B cells from peripheral blood	blood
3	chr20:52550400-52557400	Enhancers	Placenta	Placenta
4	chr20:52551800-52557000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr20:52552000-52556800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr20:52552000-52565200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr20:52552200-52557000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:52552200-52565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr20:52552400-52566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:52552600-52557400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr20:52552600-52557800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr20:52552600-52564400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr20:52552800-52556600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr20:52552800-52560200	Weak transcription	Primary T cells from cord blood	blood
15	chr20:52552800-52560200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr20:52553800-52558600	Enhancers	HepG2	liver
17	chr20:52554000-52557000	Weak transcription	Fetal Stomach	stomach
18	chr20:52554200-52559200	Enhancers	K562	blood
19	chr20:52554600-52560000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr20:52554600-52561000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr20:52554800-52565000	Weak transcription	Spleen	Spleen
22	chr20:52555000-52557600	Enhancers	Colonic Mucosa	Colon
23	chr20:52555000-52557600	Enhancers	Stomach Mucosa	stomach
24	chr20:52555200-52556800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr20:52555200-52559400	Enhancers	Placenta Amnion	Placenta Amnion
26	chr20:52555400-52556600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr20:52555400-52556600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr20:52555400-52557000	Enhancers	HSMM	muscle
29	chr20:52555400-52557000	Enhancers	NHEK	skin
30	chr20:52555400-52557200	Enhancers	Brain Hippocampus Middle	brain
31	chr20:52555400-52557400	Enhancers	NHLF	lung
32	chr20:52555400-52557600	Enhancers	Brain Cingulate Gyrus	brain
33	chr20:52555400-52557600	Enhancers	Duodenum Mucosa	Duodenum
34	chr20:52555400-52557800	Enhancers	HMEC	breast
35	chr20:52555400-52559400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr20:52555400-52561000	Enhancers	Fetal Heart	heart
37	chr20:52555600-52556600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr20:52555600-52556800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr20:52555600-52556800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr20:52555600-52556800	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr20:52555600-52556800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr20:52555600-52556800	Enhancers	Stomach Smooth Muscle	stomach
43	chr20:52555600-52557000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr20:52555600-52557000	Weak transcription	Right Atrium	heart
45	chr20:52555600-52557200	Enhancers	Brain Angular Gyrus	brain
46	chr20:52555600-52557400	Enhancers	Osteobl	bone
47	chr20:52555600-52557600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr20:52555800-52556600	Enhancers	H9 Cell Line	embryonic stem cell
49	chr20:52555800-52556600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr20:52555800-52556600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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