Variant report

Variant	rs16998568
Chromosome Location	chr20:52551750-52551751
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	POLR2A	chr20:52550948-52551810	K562	blood:	n/a	n/a
2	RCOR1	chr20:52550573-52551996	GM12878	blood:	n/a	n/a
3	POLR2A	chr20:52550934-52552192	GM12878	blood:	n/a	n/a
4	IKZF1	chr20:52551010-52552066	GM12878	blood:	n/a	n/a
5	POLR2A	chr20:52549954-52552610	Raji	blood:	n/a	n/a
6	STAT5A	chr20:52550999-52552050	GM12878	blood:	n/a	chr20:52551347-52551359
7	MXI1	chr20:52550709-52552101	GM12878	blood:	n/a	n/a
8	MAX	chr20:52551554-52552187	K562	blood:	n/a	n/a
9	ZMIZ1	chr20:52550925-52552001	K562	blood:	n/a	n/a
10	JUND	chr20:52550903-52552362	K562	blood:	n/a	chr20:52551342-52551351 chr20:52551399-52551408 chr20:52551068-52551075
11	POLR2A	chr20:52550879-52552585	GM12878	blood:	n/a	n/a
12	TEAD4	chr20:52550818-52552137	K562	blood:	n/a	n/a
13	MAX	chr20:52550975-52552505	GM12878	blood:	n/a	n/a
14	SMC3	chr20:52550986-52552122	GM12878	blood:	n/a	n/a
15	MAX	chr20:52550911-52552202	NB4	blood:	n/a	n/a
16	RUNX3	chr20:52550947-52551898	GM12878	blood:	n/a	chr20:52551313-52551322
17	HCFC1	chr20:52550944-52552107	K562	blood:	n/a	n/a
18	IRF1	chr20:52551012-52552090	K562	blood:	n/a	chr20:52551823-52551837
19	POLR2A	chr20:52551690-52552154	GM12891	blood:	n/a	n/a
20	POLR2A	chr20:52550944-52551772	K562	blood:	n/a	n/a
21	POLR2A	chr20:52551359-52551755	K562	blood:	n/a	n/a
22	STAT3	chr20:52551084-52551900	GM12878	blood:	n/a	chr20:52551347-52551359
23	POLR2A	chr20:52549898-52552197	GM12878	blood:	n/a	n/a
24	MAX	chr20:52551729-52552263	K562	blood:	n/a	n/a
25	POLR2A	chr20:52550959-52551847	HL-60	blood:	n/a	n/a
26	NR2F2	chr20:52550799-52551784	K562	blood:	n/a	n/a
27	RCOR1	chr20:52551348-52552012	K562	blood:	n/a	n/a
28	RCOR1	chr20:52550716-52552425	K562	blood:	n/a	n/a
29	NFIC	chr20:52550853-52552010	GM12878	blood:	n/a	n/a
30	WRNIP1	chr20:52551611-52552119	GM12878	blood:	n/a	n/a
31	MTA3	chr20:52551028-52552001	GM12878	blood:	n/a	n/a
32	GATA1	chr20:52550989-52552057	PBDE	blood:	n/a	chr20:52551591-52551599 chr20:52551068-52551077 chr20:52551581-52551598 chr20:52551398-52551408
33	CEBPD	chr20:52551174-52551831	K562	blood:	n/a	n/a
34	MTA3	chr20:52550896-52552643	GM12878	blood:	n/a	n/a
35	STAT5A	chr20:52551085-52551830	K562	blood:	n/a	chr20:52551347-52551359
36	NFIC	chr20:52550888-52552084	GM12878	blood:	n/a	n/a
37	RFX5	chr20:52551736-52551936	GM12878	blood:	n/a	n/a
38	PML	chr20:52550764-52552176	GM12878	blood:	n/a	n/a
39	MYC	chr20:52551087-52552537	K562	blood:	n/a	n/a
40	EP300	chr20:52550812-52552160	K562	blood:	n/a	chr20:52551780-52551794 chr20:52550845-52550859 chr20:52551534-52551543 chr20:52550844-52550858 chr20:52550843-52550857 chr20:52550842-52550856
41	TEAD4	chr20:52551708-52552713	A549	lung:	n/a	n/a
42	TBP	chr20:52550904-52552007	GM12878	blood:	n/a	n/a
43	TEAD4	chr20:52551085-52551790	K562	blood:	n/a	n/a
44	TBL1XR1	chr20:52550832-52551762	K562	blood:	n/a	n/a
45	MYC	chr20:52550937-52552571	K562	blood:	n/a	n/a
46	POLR2A	chr20:52550880-52552195	NB4	blood:	n/a	n/a
47	RUNX3	chr20:52550833-52552097	GM12878	blood:	n/a	chr20:52551313-52551322
48	CHD2	chr20:52551059-52552022	GM12878	blood:	n/a	n/a
49	EBF1	chr20:52551486-52551785	GM12878	blood:	n/a	n/a
50	POLR2A	chr20:52550634-52552139	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:52194896..52195863-chr20:52550123..52551759,4	MCF-7	breast:
2	chr20:52367670..52370398-chr20:52548161..52552939,6	K562	blood:
3	chr20:52521138..52522738-chr20:52550916..52552554,2	K562	blood:
4	chr17:57109264..57111051-chr20:52551167..52554043,2	MCF-7	breast:
5	chr20:52551745..52571491-chr20:55837843..55848700,39	MCF-7	breast:
6	chr20:52469682..52472418-chr20:52551027..52553100,2	K562	blood:
7	chr20:52551078..52553567-chr20:55847607..55851332,6	MCF-7	breast:
8	chr17:57921749..57924885-chr20:52550467..52553589,3	MCF-7	breast:
9	chr20:52548692..52552101-chr20:55839394..55841994,3	MCF-7	breast:
10	chr20:52368056..52371228-chr20:52549159..52552395,4	K562	blood:
11	chr20:52203936..52206746-chr20:52550032..52552286,2	K562	blood:
12	chr20:52550372..52553297-chr20:52685903..52688143,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236352	TF binding region
ENSG00000064787	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16998567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16998577	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16998583	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs886855	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52538400-52553400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:52543600-52556000	Weak transcription	Aorta	Aorta
3	chr20:52543800-52555000	Weak transcription	Stomach Mucosa	stomach
4	chr20:52544800-52552000	Weak transcription	Lung	lung
5	chr20:52549000-52558800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr20:52549400-52553800	Enhancers	Primary hematopoietic stem cells	blood
7	chr20:52549800-52552600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr20:52550000-52552600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr20:52550000-52552600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr20:52550000-52552600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr20:52550000-52552600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr20:52550000-52552600	Enhancers	HUVEC	blood vessel
13	chr20:52550000-52552800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr20:52550000-52552800	Enhancers	Primary T cells from cord blood	blood
15	chr20:52550000-52556800	Enhancers	Primary B cells from peripheral blood	blood
16	chr20:52550200-52552000	Flanking Active TSS	K562	blood
17	chr20:52550200-52552200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr20:52550200-52552200	Enhancers	Fetal Stomach	stomach
19	chr20:52550200-52552200	Flanking Active TSS	GM12878-XiMat	blood
20	chr20:52550200-52552200	Enhancers	NHDF-Ad	bronchial
21	chr20:52550200-52552600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:52550200-52552600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr20:52550200-52552600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr20:52550200-52552600	Enhancers	Fetal Muscle Leg	muscle
25	chr20:52550200-52552600	Enhancers	Fetal Thymus	thymus
26	chr20:52550200-52553000	Enhancers	Primary T cells fromperipheralblood	blood
27	chr20:52550200-52555000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr20:52550400-52551800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr20:52550400-52552200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr20:52550400-52552200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr20:52550400-52552600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr20:52550400-52552600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr20:52550400-52557400	Enhancers	Placenta	Placenta
34	chr20:52550600-52551800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr20:52550600-52552200	Enhancers	Fetal Kidney	kidney
36	chr20:52550600-52552400	Enhancers	Fetal Lung	lung
37	chr20:52550600-52552400	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr20:52550600-52552600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr20:52550600-52552600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr20:52550600-52552600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr20:52550600-52552600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr20:52550600-52552600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr20:52550600-52552600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr20:52550800-52552000	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr20:52550800-52552000	Enhancers	A549	lung
46	chr20:52550800-52552000	Enhancers	HMEC	breast
47	chr20:52550800-52552000	Enhancers	NH-A	brain
48	chr20:52550800-52552200	Enhancers	NHLF	lung
49	chr20:52550800-52552600	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr20:52550800-52552600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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