Variant report

Variant	rs13048151
Chromosome Location	chr21:45580129-45580130
allele	C/G
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	NFIC	chr21:45578498-45580543	GM12878	blood:	n/a	chr21:45579544-45579572
2	FOXM1	chr21:45579321-45580130	GM12878	blood:	n/a	n/a
3	POLR2A	chr21:45578629-45581133	GM18526	blood:	n/a	n/a
4	POLR2A	chr21:45572928-45581556	GM12878	blood:	n/a	n/a
5	POLR2A	chr21:45578463-45581426	GM12892	blood:	n/a	n/a
6	POLR2A	chr21:45579894-45580197	K562	blood:	n/a	n/a
7	JUN	chr21:45579619-45580160	K562	blood:	n/a	n/a
8	RELA	chr21:45579082-45580400	GM12891	blood:	n/a	n/a
9	POLR2A	chr21:45578519-45581150	GM12892	blood:	n/a	n/a
10	NR3C1	chr21:45579961-45580500	A549	lung:	n/a	n/a
11	MYC	chr21:45580093-45580324	GM12878	blood:	n/a	n/a
12	CTCF	chr21:45579990-45580181	GM12891	blood:	n/a	n/a
13	STAT5A	chr21:45578807-45580184	GM12878	blood:	n/a	chr21:45579511-45579523 chr21:45579506-45579518 chr21:45579964-45579976
14	NR3C1	chr21:45579693-45580240	A549	lung:	n/a	n/a
15	RELA	chr21:45579314-45580131	GM12892	blood:	n/a	n/a
16	MYC	chr21:45580078-45580450	MCF-7	breast:	n/a	n/a
17	CTCF	chr21:45579910-45580430	GM19239	blood:	n/a	n/a
18	POU2F2	chr21:45579519-45580165	GM12878	blood:	n/a	chr21:45579641-45579653 chr21:45579534-45579546
19	POLR2A	chr21:45579924-45580380	HepG2	liver:	n/a	n/a
20	PML	chr21:45578623-45580274	GM12878	blood:	n/a	n/a
21	CHD2	chr21:45578588-45581136	GM12878	blood:	n/a	n/a
22	ATF2	chr21:45579351-45580177	GM12878	blood:	n/a	n/a
23	TAF1	chr21:45579652-45580180	GM12892	blood:	n/a	n/a
24	EBF1	chr21:45579562-45580163	GM12878	blood:	n/a	n/a
25	SP1	chr21:45579554-45580161	GM12878	blood:	n/a	chr21:45579964-45579978
26	MTA3	chr21:45579576-45581093	GM12878	blood:	n/a	n/a
27	RUNX3	chr21:45578995-45580183	GM12878	blood:	n/a	n/a
28	CHD1	chr21:45578993-45580369	GM12878	blood:	n/a	n/a
29	POLR2A	chr21:45578547-45581170	HL-60	blood:	n/a	n/a
30	POLR2A	chr21:45576498-45581335	GM12891	blood:	n/a	n/a
31	POLR2A	chr21:45578763-45581143	GM12891	blood:	n/a	n/a
32	EBF1	chr21:45579140-45581393	GM12878	blood:	n/a	chr21:45581234-45581247 chr21:45581235-45581245 chr21:45581236-45581245 chr21:45580762-45580772
33	POLR2A	chr21:45578806-45581049	GM15510	blood:	n/a	n/a
34	MTA3	chr21:45578504-45581427	GM12878	blood:	n/a	n/a
35	POLR2A	chr21:45578462-45581396	GM12892	blood:	n/a	n/a
36	POLR2A	chr21:45578579-45581303	HL-60	blood:	n/a	n/a
37	POLR2A	chr21:45578637-45581350	GM12878	blood:	n/a	n/a
38	POLR2A	chr21:45579234-45580153	NB4	blood:	n/a	n/a
39	TAF1	chr21:45579475-45580152	GM12878	blood:	n/a	n/a
40	POLR2A	chr21:45578640-45581161	GM12878	blood:	n/a	n/a
41	POLR2A	chr21:45578680-45581072	GM12878	blood:	n/a	n/a
42	MYC	chr21:45580012-45580169	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr21:45578594-45581129	GM18951	blood:	n/a	n/a
44	POLR2A	chr21:45578510-45581471	GM12878	blood:	n/a	n/a
45	POLR2A	chr21:45578570-45581070	GM12892	blood:	n/a	n/a
46	POLR2A	chr21:45578683-45581388	GM19193	blood:	n/a	n/a
47	POLR2A	chr21:45578673-45581415	GM12891	blood:	n/a	n/a
48	POLR2A	chr21:45578761-45581407	GM12891	blood:	n/a	n/a
49	FOXM1	chr21:45579021-45580183	GM12878	blood:	n/a	n/a
50	POLR2A	chr21:45578782-45581098	GM10847	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:45551834..45580791-chr21:45711953..45732193,97	MCF-7	breast:
2	chr21:45577492..45580364-chr21:45620942..45622616,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ICOSLG-6	chr21:45578913-45580684	XLOC_014110

Variant related genes	Relation type
ENSG00000225331	TF binding region
ENSG00000232124	Chromatin interaction
ENSG00000141959	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12626547	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13047186	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838504	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2838507	0.83[ASN][1000 genomes]
rs34137354	0.80[EUR][1000 genomes]
rs34708237	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35189635	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818884	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818885	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57683928	0.80[EUR][1000 genomes]
rs62226731	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS 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 target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv913890	chr21:45482950-45603746	Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv459294	chr21:45499171-45595060	Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv587722	chr21:45499171-45595060	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv913891	chr21:45508561-45588518	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv913892	chr21:45508561-45595060	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv913893	chr21:45508561-45603746	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv913894	chr21:45508561-45627976	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv913895	chr21:45528919-45595060	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer 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	31 gene(s)	inside rSNPs	diseases
14	nsv913896	chr21:45528919-45603746	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
15	nsv913897	chr21:45528919-45640139	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
17	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
18	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
19	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS 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	74 gene(s)	inside rSNPs	diseases
20	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
21	nsv1065479	chr21:45571324-45617878	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv913899	chr21:45577102-45611950	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	nsv913900	chr21:45577102-45640139	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13048151	PWP2	Cis_1M	lymphoblastoid	RTeQTL
rs13048151	PWP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45561000-45584400	Weak transcription	Aorta	Aorta
2	chr21:45565400-45580600	Weak transcription	Brain Germinal Matrix	brain
3	chr21:45571000-45582600	Weak transcription	Ovary	ovary
4	chr21:45573800-45580400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr21:45575400-45580200	Weak transcription	NHLF	lung
6	chr21:45575400-45580400	Weak transcription	NHDF-Ad	bronchial
7	chr21:45575400-45583400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr21:45575400-45586000	Weak transcription	Fetal Lung	lung
9	chr21:45575400-45592000	Weak transcription	Fetal Brain Female	brain
10	chr21:45575600-45584800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr21:45576000-45580400	Weak transcription	Psoas Muscle	Psoas
12	chr21:45576000-45580600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr21:45576600-45580200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr21:45576600-45580600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr21:45576600-45580600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr21:45576600-45581200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr21:45576800-45580400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr21:45576800-45580600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr21:45577000-45580200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr21:45577200-45580600	Enhancers	Fetal Muscle Trunk	muscle
21	chr21:45577200-45581000	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr21:45577600-45581400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr21:45578600-45580200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:45578600-45580200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr21:45578600-45580400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr21:45578600-45580600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr21:45578800-45580200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr21:45578800-45580200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr21:45578800-45580200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr21:45578800-45580200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr21:45578800-45580400	Flanking Active TSS	Thymus	Thymus
32	chr21:45578800-45581400	Flanking Active TSS	GM12878-XiMat	blood
33	chr21:45579000-45580200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr21:45579000-45580200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr21:45579000-45580200	Enhancers	Brain Substantia Nigra	brain
36	chr21:45579000-45580200	Flanking Active TSS	Fetal Thymus	thymus
37	chr21:45579000-45580200	Active TSS	Rectal Smooth Muscle	rectum
38	chr21:45579000-45580400	Enhancers	HSMMtube	muscle
39	chr21:45579000-45580800	Enhancers	HUVEC	blood vessel
40	chr21:45579000-45581000	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr21:45579000-45581200	Enhancers	Lung	lung
42	chr21:45579200-45580200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr21:45579200-45580200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr21:45579200-45580800	Enhancers	Fetal Intestine Small	intestine
45	chr21:45579200-45580800	Enhancers	Stomach Mucosa	stomach
46	chr21:45579200-45581000	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr21:45579200-45581200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr21:45579400-45580400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr21:45579400-45580400	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr21:45579400-45580400	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links