Variant report

Variant	rs2838512
Chromosome Location	chr21:45595124-45595125
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	MEF2A	chr21:45595062-45595448	GM12878	blood:	n/a	chr21:45595188-45595196
2	RELA	chr21:45594914-45595491	GM15510	blood:	n/a	n/a
3	PML	chr21:45594743-45595589	GM12878	blood:	n/a	n/a
4	MTA3	chr21:45594844-45595561	GM12878	blood:	n/a	n/a
5	ELF1	chr21:45594890-45595459	GM12878	blood:	n/a	chr21:45595235-45595246 chr21:45595274-45595286
6	BCLAF1	chr21:45594904-45595492	GM12878	blood:	n/a	chr21:45595189-45595198
7	POU2F2	chr21:45594927-45595406	GM12878	blood:	n/a	n/a
8	BCLAF1	chr21:45594918-45595509	GM12878	blood:	n/a	chr21:45595189-45595198
9	TCF12	chr21:45594995-45595482	GM12878	blood:	n/a	n/a
10	STAT5A	chr21:45595090-45595361	GM12878	blood:	n/a	chr21:45595189-45595200 chr21:45595229-45595237
11	YY1	chr21:45595096-45595522	GM12892	blood:	n/a	chr21:45595278-45595287
12	MAZ	chr21:45594962-45595442	GM12878	blood:	n/a	chr21:45595279-45595289
13	SPI1	chr21:45594925-45595492	GM12891	blood:	n/a	chr21:45595208-45595221 chr21:45595189-45595198 chr21:45595185-45595194
14	PAX5	chr21:45595081-45595409	GM12892	blood:	n/a	chr21:45595352-45595361 chr21:45595356-45595365 chr21:45595186-45595195 chr21:45595350-45595359 chr21:45595189-45595198
15	STAT1	chr21:45595110-45595382	GM12878	blood:	n/a	chr21:45595189-45595200 chr21:45595229-45595237
16	TBL1XR1	chr21:45594763-45595445	GM12878	blood:	n/a	n/a
17	EBF1	chr21:45594836-45595469	GM12878	blood:	n/a	n/a
18	SP1	chr21:45594963-45595451	GM12878	blood:	n/a	chr21:45595279-45595291 chr21:45595274-45595283 chr21:45595280-45595294 chr21:45595275-45595284
19	TCF3	chr21:45595013-45595390	GM12878	blood:	n/a	n/a
20	SPI1	chr21:45594697-45595723	GM12878	blood:	n/a	chr21:45595208-45595221 chr21:45595189-45595198 chr21:45595185-45595194
21	ZNF384	chr21:45595020-45595197	GM12878	blood:	n/a	n/a
22	RELA	chr21:45594999-45595429	GM19099	blood:	n/a	n/a
23	BHLHE40	chr21:45594730-45595487	GM12878	blood:	n/a	chr21:45595248-45595264
24	IRF4	chr21:45594903-45595498	GM12878	blood:	n/a	n/a
25	NFIC	chr21:45594894-45595604	GM12878	blood:	n/a	n/a
26	SPI1	chr21:45594869-45595525	GM12891	blood:	n/a	chr21:45595208-45595221 chr21:45595189-45595198 chr21:45595185-45595194
27	BATF	chr21:45595030-45595354	GM12878	blood:	n/a	n/a
28	ATF2	chr21:45594989-45595457	GM12878	blood:	n/a	n/a
29	IRF4	chr21:45594852-45595373	GM12878	blood:	n/a	n/a
30	RUNX3	chr21:45594628-45595496	GM12878	blood:	n/a	n/a
31	MAX	chr21:45594731-45595457	GM12878	blood:	n/a	chr21:45595279-45595289
32	CHD2	chr21:45594989-45595395	GM12878	blood:	n/a	n/a
33	EBF1	chr21:45594988-45595292	GM12878	blood:	n/a	n/a
34	EP300	chr21:45594954-45595429	GM12878	blood:	n/a	chr21:45595184-45595198
35	CHD1	chr21:45594922-45595483	GM12878	blood:	n/a	n/a
36	POLR2A	chr21:45594992-45595553	HL-60	blood:	n/a	n/a
37	ELF1	chr21:45595119-45595457	GM12878	blood:	n/a	chr21:45595235-45595246 chr21:45595274-45595286
38	POU2F2	chr21:45595104-45595442	GM12878	blood:	n/a	n/a
39	PAX5	chr21:45595099-45595421	GM12878	blood:	n/a	chr21:45595352-45595361 chr21:45595356-45595365 chr21:45595186-45595195 chr21:45595350-45595359 chr21:45595189-45595198
40	CEBPB	chr21:45594967-45595692	GM12878	blood:	n/a	n/a
41	USF2	chr21:45594675-45595300	GM12878	blood:	n/a	chr21:45595248-45595264
42	POLR2A	chr21:45594846-45595580	GM12892	blood:	n/a	n/a
43	RELA	chr21:45594721-45595427	GM18951	blood:	n/a	n/a
44	EP300	chr21:45594962-45595460	GM12878	blood:	n/a	chr21:45595184-45595198
45	FOXM1	chr21:45594929-45595522	GM12878	blood:	n/a	n/a
46	BCL11A	chr21:45595063-45595453	GM12878	blood:	n/a	chr21:45595189-45595198
47	PAX5	chr21:45595063-45595450	GM12878	blood:	n/a	chr21:45595352-45595361 chr21:45595356-45595365 chr21:45595186-45595195 chr21:45595350-45595359 chr21:45595189-45595198
48	EGR1	chr21:45595047-45595428	GM12878	blood:	n/a	chr21:45595276-45595289 chr21:45595275-45595290 chr21:45595276-45595286 chr21:45595276-45595289 chr21:45595276-45595289 chr21:45595277-45595286 chr21:45595273-45595287 chr21:45595276-45595289 chr21:45595277-45595288 chr21:45595275-45595289 chr21:45595352-45595361 chr21:45595350-45595359
49	STAT5A	chr21:45594633-45595588	GM12878	blood:	n/a	chr21:45595189-45595200 chr21:45595229-45595237
50	POLR2A	chr21:45594627-45595581	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:45551956..45555178-chr21:45594619..45596938,3	MCF-7	breast:
2	chr21:45590531..45598113-chr21:45625237..45630055,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237604	TF binding region
ENSG00000267913	TF binding region
ENSG00000160221	Chromatin interaction
ENSG00000232698	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1005046	0.83[CEU][hapmap]
rs1131999	0.80[GIH][hapmap]
rs2020945	0.81[GIH][hapmap]
rs2071142	0.81[GIH][hapmap]
rs2071143	0.81[GIH][hapmap]
rs2243999	0.81[GIH][hapmap]
rs2251267	0.81[GIH][hapmap]
rs2838490	0.81[GIH][hapmap]
rs2838491	0.81[GIH][hapmap]
rs2838502	0.81[GIH][hapmap]
rs2838511	0.89[CEU][hapmap]
rs2838513	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34232577	0.96[ASN][1000 genomes]
rs4819376	0.81[GIH][hapmap]
rs4819384	1.00[JPT][hapmap]
rs7280558	0.81[GIH][hapmap]
rs756554	0.81[GIH][hapmap]
rs968714	0.81[GIH][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2838512	KRTAP10-1	cis	cerebellum	SCAN
rs2838512	PWP2	cis	parietal	SCAN
rs2838512	TRAPPC10	cis	cerebellum	SCAN
rs2838512	PWP2	cis	lymphoblastoid	seeQTL
rs2838512	C21orf33	cis	parietal	SCAN
rs2838512	PWP2	Cis_1M	lymphoblastoid	RTeQTL
rs2838512	ABCG1	cis	cerebellum	SCAN

Chromatin state (count:42 , 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	chr21:45591200-45595400	Enhancers	Primary B cells from cord blood	blood
4	chr21:45591800-45596000	Weak transcription	Fetal Intestine Small	intestine
5	chr21:45592000-45598000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr21:45593200-45595200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:45593200-45596400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr21:45593200-45601000	Weak transcription	Right Atrium	heart
9	chr21:45593400-45595200	Enhancers	Primary B cells from peripheral blood	blood
10	chr21:45593400-45595600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr21:45593400-45595800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr21:45593400-45595800	Weak transcription	Esophagus	oesophagus
13	chr21:45593400-45595800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr21:45593400-45596000	Enhancers	Colonic Mucosa	Colon
15	chr21:45593400-45596000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr21:45593400-45602200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr21:45593400-45605000	Weak transcription	Small Intestine	intestine
18	chr21:45593600-45595200	Weak transcription	Gastric	stomach
19	chr21:45593600-45596000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr21:45593600-45596200	Weak transcription	Lung	lung
21	chr21:45593600-45596600	Enhancers	Fetal Thymus	thymus
22	chr21:45593600-45604800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr21:45594000-45595200	Weak transcription	Placenta	Placenta
24	chr21:45594000-45595400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr21:45594000-45595600	Weak transcription	Stomach Mucosa	stomach
26	chr21:45594000-45595800	Weak transcription	Brain Anterior Caudate	brain
27	chr21:45594000-45596200	Weak transcription	Brain Hippocampus Middle	brain
28	chr21:45594200-45595800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr21:45594200-45595800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr21:45594200-45596000	Weak transcription	Pancreas	Pancrea
31	chr21:45594400-45596600	Enhancers	Primary hematopoietic stem cells	blood
32	chr21:45594600-45596600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr21:45594800-45595400	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr21:45594800-45596000	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr21:45594800-45596400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr21:45595000-45595400	Enhancers	Right Ventricle	heart
37	chr21:45595000-45595400	Enhancers	GM12878-XiMat	blood
38	chr21:45595000-45595400	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr21:45595000-45595800	Weak transcription	Adipose Nuclei	Adipose
40	chr21:45595000-45595800	Weak transcription	Fetal Muscle Leg	muscle
41	chr21:45595000-45595800	Weak transcription	Spleen	Spleen
42	chr21:45595000-45597600	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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