Variant report

Variant	rs984497
Chromosome Location	chr20:1455810-1455811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:45 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr20:1455578-1455856	T-47D	breast:	n/a	n/a
2	CTCF	chr20:1455660-1455810	HCPEpiC	choroid plexus:	n/a	n/a
3	TEAD4	chr20:1455750-1456275	K562	blood:	n/a	n/a
4	RAD21	chr20:1455483-1455930	A549	lung:	n/a	n/a
5	CTCF	chr20:1455680-1455830	HEK293	kidney:	n/a	n/a
6	CTCF	chr20:1455523-1455875	GM12878	blood:	n/a	n/a
7	RAD21	chr20:1455554-1455830	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr20:1455539-1455880	NHEK	skin:	n/a	n/a
9	MAX	chr20:1455604-1455867	NB4	blood:	n/a	n/a
10	CTCF	chr20:1455564-1455978	MCF-7	breast:	n/a	n/a
11	CTCF	chr20:1455651-1455865	A549	lung:	n/a	n/a
12	CTCF	chr20:1455476-1456235	HCT-116	colon:	n/a	n/a
13	SMC3	chr20:1455618-1455873	GM12878	blood:	n/a	n/a
14	RAD21	chr20:1455577-1455834	A549	lung:	n/a	n/a
15	CTCF	chr20:1455502-1455955	MCF-7	breast:	n/a	n/a
16	RAD21	chr20:1455460-1455939	A549	lung:	n/a	n/a
17	CTCF	chr20:1455660-1455810	HEK293	kidney:	n/a	n/a
18	RAD21	chr20:1455480-1456044	HCT-116	colon:	n/a	n/a
19	CTCF	chr20:1455660-1455890	GM12868	blood:	n/a	n/a
20	CTCF	chr20:1455481-1456089	HCT-116	colon:	n/a	n/a
21	CTCF	chr20:1455660-1455810	MCF-7	breast:	n/a	n/a
22	CTCF	chr20:1455660-1455810	GM12872	blood:	n/a	n/a
23	FOS	chr20:1455364-1455838	MCF10A-Er-Src	breast:	n/a	n/a
24	MYC	chr20:1455439-1455812	MCF10A-Er-Src	breast:	n/a	n/a
25	CTCF	chr20:1455680-1455830	HUVEC	blood vessel:	n/a	n/a
26	SMC3	chr20:1455523-1455860	Hela-S3	cervix:	n/a	n/a
27	ZNF143	chr20:1455785-1456217	H1-hESC	embryonic stem cell:	n/a	n/a
28	RAD21	chr20:1455567-1455851	H1-hESC	embryonic stem cell:	n/a	n/a
29	USF1	chr20:1455762-1456288	HCT-116	colon:	n/a	chr20:1456044-1456055
30	CTCF	chr20:1455760-1455910	RPTEC	kidney:	n/a	n/a
31	USF1	chr20:1455807-1456224	ECC-1	luminal epithelium:	n/a	chr20:1456044-1456055
32	RAD21	chr20:1455580-1455888	GM12878	blood:	n/a	n/a
33	CTCF	chr20:1455455-1455946	A549	lung:	n/a	n/a
34	RAD21	chr20:1455599-1455815	HepG2	liver:	n/a	n/a
35	RAD21	chr20:1455525-1455935	H1-hESC	embryonic stem cell:	n/a	n/a
36	RAD21	chr20:1455497-1456138	HCT-116	colon:	n/a	n/a
37	CTCF	chr20:1455595-1455812	GM19238	blood:	n/a	n/a
38	CTCF	chr20:1455554-1455863	A549	lung:	n/a	n/a
39	RAD21	chr20:1455538-1455866	GM12878	blood:	n/a	n/a
40	ZNF143	chr20:1455640-1456082	GM12878	blood:	n/a	n/a
41	MYC	chr20:1455433-1455837	MCF10A-Er-Src	breast:	n/a	n/a
42	CTCF	chr20:1455680-1455830	HMEC	breast:	n/a	n/a
43	CTCF	chr20:1455412-1456079	A549	lung:	n/a	n/a
44	CTCF	chr20:1455660-1455810	A549	lung:	n/a	n/a
45	RAD21	chr20:1455551-1455869	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:1455226..1456302-chr20:1484020..1485065,7	MCF-7	breast:
2	chr20:1455104..1456167-chr20:1483834..1485085,9	MCF-7	breast:

No data

Variant related genes	Relation type
NSFL1C	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12480584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481007	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs16994239	1.00[JPT][hapmap]
rs17793360	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	1.00[JPT][hapmap]
rs1884393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs2064645	1.00[JPT][hapmap]
rs2064646	1.00[JPT][hapmap]
rs2273321	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2873522	1.00[JPT][hapmap]
rs3829697	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275406	1.00[ASN][1000 genomes]
rs6033935	1.00[JPT][hapmap]
rs6105101	1.00[JPT][hapmap]
rs6109984	1.00[JPT][hapmap]
rs6109989	1.00[JPT][hapmap]
rs8118710	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8123855	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984498	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs984497	KLF5	trans	lymphoblastoid	seeQTL
rs984497	ASRGL1	trans	lymphoblastoid	seeQTL
rs984497	PSMF1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1448200-1457400	Weak transcription	Spleen	Spleen
2	chr20:1448200-1459000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr20:1450400-1459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:1450400-1459000	Weak transcription	Lung	lung
5	chr20:1450800-1456200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr20:1450800-1458200	Genic enhancers	Primary monocytes fromperipheralblood	blood
7	chr20:1451200-1456000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr20:1451600-1459000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr20:1452000-1459000	Weak transcription	HUVEC	blood vessel
10	chr20:1452000-1459000	Weak transcription	NH-A	brain
11	chr20:1454200-1458000	Genic enhancers	Monocytes-CD14+_RO01746	blood
12	chr20:1454200-1458800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:1454200-1458800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr20:1454200-1460800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr20:1454400-1456000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
16	chr20:1454400-1459000	Weak transcription	Osteobl	bone
17	chr20:1454400-1460400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr20:1454400-1460600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr20:1454400-1460600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr20:1454600-1458000	Enhancers	HMEC	breast
21	chr20:1454800-1456000	Weak transcription	Fetal Intestine Small	intestine
22	chr20:1454800-1459000	Weak transcription	A549	lung
23	chr20:1455200-1456600	Enhancers	NHEK	skin
24	chr20:1455600-1456200	Enhancers	Esophagus	oesophagus
25	chr20:1455600-1456200	Enhancers	Stomach Mucosa	stomach
26	chr20:1455600-1458000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr20:1455600-1458400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr20:1455600-1461600	Enhancers	Placenta	Placenta
29	chr20:1455800-1456000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr20:1455800-1456000	Enhancers	Duodenum Mucosa	Duodenum
31	chr20:1455800-1456200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr20:1455800-1456200	Enhancers	K562	blood
33	chr20:1455800-1456400	Enhancers	Fetal Intestine Large	intestine
34	chr20:1455800-1458000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links