Variant report

Variant	rs2039273
Chromosome Location	chr21:45595932-45595933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr21:45595742-45596348	GM12878	blood:	n/a	n/a
2	TCF12	chr21:45595732-45596725	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr21:45595796-45596614	MCF-7	breast:	n/a	n/a
4	TCF12	chr21:45595920-45596623	ECC-1	luminal epithelium:	n/a	n/a
5	NR2F2	chr21:45595780-45596531	MCF-7	breast:	n/a	n/a
6	GATA3	chr21:45595831-45596425	MCF-7	breast:	n/a	n/a
7	HNF4G	chr21:45595804-45596369	HepG2	liver:	n/a	chr21:45596119-45596134
8	NR2F2	chr21:45595809-45596534	MCF-7	breast:	n/a	n/a
9	PAX5	chr21:45595930-45596177	GM12878	blood:	n/a	n/a
10	TCF12	chr21:45595913-45596342	GM12878	blood:	n/a	n/a
11	POLR2A	chr21:45595794-45596705	GM12878	blood:	n/a	n/a
12	SPI1	chr21:45595852-45596347	GM12878	blood:	n/a	n/a
13	MAX	chr21:45595912-45596400	MCF-7	breast:	n/a	n/a
14	MYBL2	chr21:45595886-45596462	HepG2	liver:	n/a	n/a
15	BRCA1	chr21:45595906-45596002	HepG2	liver:	n/a	n/a
16	ESR1	chr21:45595880-45596302	T-47D	breast:	n/a	n/a
17	ESR1	chr21:45595890-45596318	ECC-1	luminal epithelium:	n/a	n/a
18	ESR1	chr21:45595868-45596341	ECC-1	luminal epithelium:	n/a	n/a
19	RELA	chr21:45595932-45596438	GM18951	blood:	n/a	n/a
20	MYBL2	chr21:45595908-45596377	HepG2	liver:	n/a	n/a
21	HNF4G	chr21:45595926-45596339	HepG2	liver:	n/a	chr21:45596119-45596134
22	RUNX3	chr21:45595769-45596344	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45551956..45555178-chr21:45594619..45596938,3	MCF-7	breast:
2	chr21:45546961..45549200-chr21:45595303..45598230,2	K562	blood:
3	chr21:45595680..45596514-chr21:45615830..45617060,14	MCF-7	breast:
4	chr21:45595676..45596652-chr21:45615636..45617063,9	MCF-7	breast:
5	chr21:45595723..45596653-chr21:45604850..45605608,2	MCF-7	breast:
6	chr21:45595676..45596715-chr21:45615636..45617128,25	MCF-7	breast:
7	chr21:45574083..45574904-chr21:45595737..45596568,4	MCF-7	breast:
8	chr21:45595760..45596300-chr21:45714724..45715293,2	MCF-7	breast:
9	chr21:45570082..45570694-chr21:45595663..45596552,2	MCF-7	breast:
10	chr21:45595647..45596418-chr21:45663539..45664451,5	MCF-7	breast:
11	chr21:45590531..45598113-chr21:45625237..45630055,9	MCF-7	breast:
12	chr21:45595647..45596211-chr21:45663539..45664160,2	MCF-7	breast:
13	chr21:45595604..45596199-chr21:45660274..45660937,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C21orf33-1	chr21:45595563-45596336	XLOC_013966

No data

Variant related genes	Relation type
ENSG00000267913	TF binding region
ENSG00000160223	Chromatin interaction
ENSG00000160221	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000241945	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17004619	1.00[JPT][hapmap]
rs2838457	1.00[JPT][hapmap]
rs2838461	1.00[JPT][hapmap]
rs4819384	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2039273	PWP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45584200-45598800	Weak transcription	Ovary	ovary
2	chr21:45587600-45596200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr21:45591800-45596000	Weak transcription	Fetal Intestine Small	intestine
4	chr21:45592000-45598000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr21:45593200-45596400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr21:45593200-45601000	Weak transcription	Right Atrium	heart
7	chr21:45593400-45596000	Enhancers	Colonic Mucosa	Colon
8	chr21:45593400-45596000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr21:45593400-45602200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr21:45593400-45605000	Weak transcription	Small Intestine	intestine
11	chr21:45593600-45596000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr21:45593600-45596200	Weak transcription	Lung	lung
13	chr21:45593600-45596600	Enhancers	Fetal Thymus	thymus
14	chr21:45593600-45604800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr21:45594000-45596200	Weak transcription	Brain Hippocampus Middle	brain
16	chr21:45594200-45596000	Weak transcription	Pancreas	Pancrea
17	chr21:45594400-45596600	Enhancers	Primary hematopoietic stem cells	blood
18	chr21:45594600-45596600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr21:45594800-45596000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr21:45594800-45596400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr21:45595000-45597600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr21:45595200-45597000	Enhancers	Placenta	Placenta
23	chr21:45595200-45597200	Enhancers	Gastric	stomach
24	chr21:45595200-45597600	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr21:45595400-45596400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr21:45595400-45596600	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr21:45595400-45597400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr21:45595400-45597600	Flanking Active TSS	GM12878-XiMat	blood
29	chr21:45595600-45596000	Enhancers	Stomach Mucosa	stomach
30	chr21:45595600-45596400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr21:45595600-45596400	Enhancers	Right Ventricle	heart
32	chr21:45595600-45596600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr21:45595800-45596000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr21:45595800-45596000	Flanking Active TSS	HepG2	liver
35	chr21:45595800-45596200	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr21:45595800-45596200	ZNF genes & repeats	Brain Anterior Caudate	brain
37	chr21:45595800-45596600	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr21:45595800-45596600	Enhancers	Esophagus	oesophagus
39	chr21:45595800-45597200	Enhancers	Spleen	Spleen
40	chr21:45595800-45597600	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr21:45595800-45598000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr21:45595800-45598200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
43	chr21:45595800-45598400	Enhancers	Fetal Muscle Leg	muscle

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