Variant report

Variant	rs984498
Chromosome Location	chr20:1456141-1456142
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	USF2	chr20:1455935-1456210	Hela-S3	cervix:	n/a	chr20:1456044-1456055
2	TEAD4	chr20:1455850-1456237	K562	blood:	n/a	n/a
3	USF1	chr20:1455878-1456252	H1-hESC	embryonic stem cell:	n/a	chr20:1456044-1456055
4	TEAD4	chr20:1455750-1456275	K562	blood:	n/a	n/a
5	HCFC1	chr20:1455831-1456232	K562	blood:	n/a	n/a
6	POLR2A	chr20:1456077-1456262	MCF10A-Er-Src	breast:	n/a	n/a
7	USF1	chr20:1455947-1456168	SK-N-SH_RA	brain:	n/a	chr20:1456044-1456055
8	ZNF143	chr20:1455829-1456222	K562	blood:	n/a	n/a
9	USF1	chr20:1455867-1456248	ECC-1	luminal epithelium:	n/a	chr20:1456044-1456055
10	TEAD4	chr20:1455829-1456317	ECC-1	luminal epithelium:	n/a	n/a
11	CTCF	chr20:1455476-1456235	HCT-116	colon:	n/a	n/a
12	USF1	chr20:1455881-1456243	A549	lung:	n/a	chr20:1456044-1456055
13	TEAD4	chr20:1455811-1456294	H1-hESC	embryonic stem cell:	n/a	n/a
14	USF2	chr20:1455850-1456224	H1-hESC	embryonic stem cell:	n/a	chr20:1456044-1456055
15	USF1	chr20:1455913-1456141	HepG2	liver:	n/a	chr20:1456044-1456055
16	USF1	chr20:1455855-1456169	A549	lung:	n/a	chr20:1456044-1456055
17	SIX5	chr20:1455871-1456179	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZNF143	chr20:1455785-1456217	H1-hESC	embryonic stem cell:	n/a	n/a
19	USF1	chr20:1455762-1456288	HCT-116	colon:	n/a	chr20:1456044-1456055
20	MAX	chr20:1455932-1456176	H1-hESC	embryonic stem cell:	n/a	n/a
21	USF1	chr20:1455807-1456224	ECC-1	luminal epithelium:	n/a	chr20:1456044-1456055
22	USF1	chr20:1455866-1456172	H1-hESC	embryonic stem cell:	n/a	chr20:1456044-1456055
23	USF1	chr20:1455827-1456281	SK-N-SH	brain:	n/a	chr20:1456044-1456055
24	USF2	chr20:1455958-1456188	HepG2	liver:	n/a	chr20:1456044-1456055
25	USF1	chr20:1455885-1456192	A549	lung:	n/a	chr20:1456044-1456055
26	USF1	chr20:1455915-1456223	K562	blood:	n/a	chr20:1456044-1456055
27	TEAD4	chr20:1455832-1456305	H1-hESC	embryonic stem cell:	n/a	n/a
28	USF1	chr20:1455921-1456214	K562	blood:	n/a	chr20:1456044-1456055
29	USF1	chr20:1455916-1456150	A549	lung:	n/a	chr20:1456044-1456055
30	USF1	chr20:1455854-1456201	HepG2	liver:	n/a	chr20:1456044-1456055

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:

Variant related genes	Relation type
NSFL1C	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12480584	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481007	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12481707	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]
rs16994239	1.00[JPT][hapmap]
rs17793360	0.93[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs1884390	1.00[JPT][hapmap]
rs1884393	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.82[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	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[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	0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8123855	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984497	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs984498	CPXM1	cis	cerebellum	SCAN
rs984498	PSMF1	cis	parietal	SCAN

Chromatin state (count:31 , 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	chr20:1451600-1459000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr20:1452000-1459000	Weak transcription	HUVEC	blood vessel
9	chr20:1452000-1459000	Weak transcription	NH-A	brain
10	chr20:1454200-1458000	Genic enhancers	Monocytes-CD14+_RO01746	blood
11	chr20:1454200-1458800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:1454200-1458800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr20:1454200-1460800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr20:1454400-1459000	Weak transcription	Osteobl	bone
15	chr20:1454400-1460400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr20:1454400-1460600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr20:1454400-1460600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr20:1454600-1458000	Enhancers	HMEC	breast
19	chr20:1454800-1459000	Weak transcription	A549	lung
20	chr20:1455200-1456600	Enhancers	NHEK	skin
21	chr20:1455600-1456200	Enhancers	Esophagus	oesophagus
22	chr20:1455600-1456200	Enhancers	Stomach Mucosa	stomach
23	chr20:1455600-1458000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr20:1455600-1458400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr20:1455600-1461600	Enhancers	Placenta	Placenta
26	chr20:1455800-1456200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr20:1455800-1456200	Enhancers	K562	blood
28	chr20:1455800-1456400	Enhancers	Fetal Intestine Large	intestine
29	chr20:1455800-1458000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr20:1456000-1456200	Enhancers	Fetal Intestine Small	intestine
31	chr20:1456000-1459200	Strong transcription	Primary neutrophils fromperipheralblood	blood

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