Variant report

Variant	rs1228027
Chromosome Location	chr11:48042112-48042113
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	CEBPB	chr11:48041816-48042114	K562	blood:	n/a	n/a
2	CEBPB	chr11:48040899-48042185	GM12878	blood:	n/a	n/a
3	MTA3	chr11:48039972-48042630	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:48041193-48042188	GM12878	blood:	n/a	n/a
5	MTA3	chr11:48040776-48042413	GM12878	blood:	n/a	n/a
6	BCLAF1	chr11:48040874-48042270	GM12878	blood:	n/a	chr11:48041062-48041071
7	NFIC	chr11:48040564-48042164	GM12878	blood:	n/a	n/a
8	RUNX3	chr11:48040036-48042356	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:48041568-48042324	HL-60	blood:	n/a	n/a
10	ELF1	chr11:48041516-48042169	GM12878	blood:	n/a	n/a
11	NFIC	chr11:48039979-48042253	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:48041683-48042376	HL-60	blood:	n/a	n/a
13	MYC	chr11:48041543-48042487	NB4	blood:	n/a	chr11:48042327-48042337
14	STAT5A	chr11:48040136-48042222	GM12878	blood:	n/a	chr11:48040714-48040722
15	POLR2A	chr11:48040915-48042413	Raji	blood:	n/a	n/a
16	EBF1	chr11:48041637-48042351	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:48042053-48042282	GM12878	blood:	n/a	n/a
18	IRF4	chr11:48041559-48042185	GM12878	blood:	n/a	n/a
19	FOXM1	chr11:48041487-48042218	GM12878	blood:	n/a	n/a
20	SPI1	chr11:48041545-48042278	HL-60	blood:	n/a	n/a
21	FOXM1	chr11:48040730-48042218	GM12878	blood:	n/a	n/a
22	TAF1	chr11:48041610-48042125	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:48040829-48042276	GM12891	blood:	n/a	n/a
24	POU2F2	chr11:48041604-48042353	GM12891	blood:	n/a	chr11:48041840-48041855 chr11:48041843-48041851 chr11:48041843-48041853 chr11:48041843-48041852 chr11:48041843-48041853 chr11:48041844-48041851 chr11:48041841-48041852 chr11:48041836-48041857 chr11:48041842-48041852 chr11:48041842-48041854 chr11:48041838-48041856
25	BATF	chr11:48041588-48042292	GM12878	blood:	n/a	chr11:48041720-48041728
26	ATF2	chr11:48041357-48042266	GM12878	blood:	n/a	n/a
27	MAX	chr11:48041502-48042372	NB4	blood:	n/a	chr11:48042327-48042337
28	POLR2A	chr11:48040434-48042139	GM12891	blood:	n/a	n/a
29	YY1	chr11:48041636-48042194	GM12878	blood:	n/a	n/a
30	POLR2A	chr11:48041519-48042401	GM12878	blood:	n/a	n/a
31	YY1	chr11:48041185-48042276	GM12878	blood:	n/a	chr11:48041566-48041574
32	GATA1	chr11:48041145-48042128	PBDE	blood:	n/a	chr11:48041512-48041519 chr11:48041512-48041519 chr11:48041501-48041518 chr11:48041512-48041519 chr11:48041505-48041526 chr11:48041510-48041520 chr11:48041507-48041523
33	POLR2A	chr11:48039780-48042512	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:48039845-48042568	GM12891	blood:	n/a	n/a
35	RELA	chr11:48040090-48042338	GM12891	blood:	n/a	n/a
36	POU2F2	chr11:48041535-48042152	GM12878	blood:	n/a	chr11:48041840-48041855 chr11:48041843-48041851 chr11:48041843-48041853 chr11:48041843-48041852 chr11:48041843-48041853 chr11:48041844-48041851 chr11:48041841-48041852 chr11:48041836-48041857 chr11:48041842-48041852 chr11:48041842-48041854 chr11:48041838-48041856
37	POLR2A	chr11:48040259-48042513	GM12891	blood:	n/a	n/a
38	PML	chr11:48040071-48042608	GM12878	blood:	n/a	chr11:48041061-48041070
39	NFATC1	chr11:48041565-48042385	GM12878	blood:	n/a	n/a
40	RUNX3	chr11:48039992-48042429	GM12878	blood:	n/a	n/a
41	NFATC1	chr11:48040841-48042216	GM12878	blood:	n/a	n/a
42	YY1	chr11:48041593-48042221	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:48035577..48038589-chr11:48041856..48045572,3	MCF-7	breast:
2	chr11:48037574..48039959-chr11:48041081..48044491,3	K562	blood:
3	chr11:48041770..48044575-chr11:48053476..48055088,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254879	TF binding region
ENSG00000254879	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11039489	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs11039492	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs11039506	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11039507	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11039549	1.00[YRI][hapmap]
rs11039554	1.00[YRI][hapmap]
rs11822835	1.00[AMR][1000 genomes]
rs11825374	1.00[AMR][1000 genomes]
rs12272622	1.00[AMR][1000 genomes]
rs12275069	0.88[YRI][hapmap]
rs12275893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12279082	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1228003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1228011	1.00[AMR][1000 genomes]
rs1228016	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1228029	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1228037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1228045	1.00[AMR][1000 genomes]
rs1228051	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12282960	0.88[YRI][hapmap]
rs12288995	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12290640	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12293503	0.87[YRI][hapmap]
rs12294321	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12294477	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12295345	0.88[YRI][hapmap]
rs1681606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1681638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2697809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2930185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2930187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2950886	0.95[AFR][1000 genomes]
rs2950889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4387319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7102191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7941419	1.00[AMR][1000 genomes]
rs900700	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs922959	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer 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	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv528641	chr11:48004369-48043053	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
15	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
16	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48025000-48045200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr11:48027400-48044000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr11:48032400-48042600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr11:48032400-48045200	Enhancers	Primary B cells from peripheral blood	blood
5	chr11:48032600-48042800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr11:48032800-48042400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr11:48035400-48046200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:48035600-48053000	Weak transcription	Thymus	Thymus
9	chr11:48035600-48056600	Weak transcription	HSMM	muscle
10	chr11:48037400-48045200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr11:48037600-48042400	Enhancers	Brain Substantia Nigra	brain
12	chr11:48037800-48046400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:48038000-48052400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr11:48038600-48042400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:48038600-48042400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr11:48038800-48042200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr11:48038800-48042600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:48038800-48042600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr11:48038800-48045000	Enhancers	Primary hematopoietic stem cells	blood
20	chr11:48039000-48042200	Enhancers	Liver	Liver
21	chr11:48039000-48042600	Flanking Active TSS	GM12878-XiMat	blood
22	chr11:48039200-48042400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr11:48039400-48042200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr11:48039400-48042600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr11:48039600-48042800	Enhancers	Stomach Mucosa	stomach
26	chr11:48039600-48046000	Weak transcription	Hela-S3	cervix
27	chr11:48039800-48042400	Enhancers	Placenta	Placenta
28	chr11:48040000-48042400	Enhancers	Adipose Nuclei	Adipose
29	chr11:48040000-48046400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr11:48040000-48050600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:48040000-48050800	Weak transcription	Osteobl	bone
32	chr11:48040200-48046200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr11:48040400-48043600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr11:48040600-48042400	Enhancers	Brain Anterior Caudate	brain
35	chr11:48040600-48047200	Weak transcription	Right Ventricle	heart
36	chr11:48040600-48053200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr11:48040800-48042200	Enhancers	Fetal Intestine Large	intestine
38	chr11:48040800-48042400	Enhancers	Brain Cingulate Gyrus	brain
39	chr11:48040800-48042600	Enhancers	Brain Hippocampus Middle	brain
40	chr11:48040800-48044200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:48040800-48045600	Weak transcription	Fetal Muscle Leg	muscle
42	chr11:48040800-48045800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr11:48040800-48046200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:48040800-48050400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr11:48040800-48050400	Weak transcription	NH-A	brain
46	chr11:48040800-48050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:48040800-48053000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr11:48041000-48042600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr11:48041000-48043800	Enhancers	A549	lung
50	chr11:48041000-48045600	Weak transcription	Brain Germinal Matrix	brain

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