Variant report

Variant	rs1228029
Chromosome Location	chr11:48041796-48041797
allele	A/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	WRNIP1	chr11:48041710-48041911	GM12878	blood:	n/a	n/a
2	CTCF	chr11:48041684-48041937	K562	blood:	n/a	n/a
3	MYC	chr11:48041769-48042029	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr11:48040899-48042185	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:48041672-48041990	GM12878	blood:	n/a	n/a
6	MTA3	chr11:48039972-48042630	GM12878	blood:	n/a	n/a
7	POU2F2	chr11:48041504-48042110	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
8	POLR2A	chr11:48041193-48042188	GM12878	blood:	n/a	n/a
9	FOS	chr11:48041750-48042055	MCF10A-Er-Src	breast:	n/a	n/a
10	MTA3	chr11:48040776-48042413	GM12878	blood:	n/a	n/a
11	BCLAF1	chr11:48040874-48042270	GM12878	blood:	n/a	chr11:48041062-48041071
12	NFIC	chr11:48040564-48042164	GM12878	blood:	n/a	n/a
13	RAD21	chr11:48041589-48042003	GM12878	blood:	n/a	n/a
14	CTCF	chr11:48041774-48041853	GM10248	blood:	n/a	n/a
15	CTCF	chr11:48041740-48041890	GM12871	blood:	n/a	n/a
16	EBF1	chr11:48041666-48042104	GM12878	blood:	n/a	n/a
17	RUNX3	chr11:48040036-48042356	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:48041568-48042324	HL-60	blood:	n/a	n/a
19	CEBPB	chr11:48041727-48042005	GM12878	blood:	n/a	n/a
20	POU2F2	chr11:48041586-48042026	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
21	UBTF	chr11:48041747-48041846	K562	blood:	n/a	n/a
22	STAT5A	chr11:48041607-48042024	GM12878	blood:	n/a	n/a
23	SPI1	chr11:48041696-48042029	GM12878	blood:	n/a	n/a
24	ELF1	chr11:48041516-48042169	GM12878	blood:	n/a	n/a
25	NFIC	chr11:48039979-48042253	GM12878	blood:	n/a	n/a
26	CTCF	chr11:48041680-48041830	GM12874	blood:	n/a	n/a
27	CTCF	chr11:48041740-48041890	GM12866	blood:	n/a	n/a
28	POLR2A	chr11:48041683-48042376	HL-60	blood:	n/a	n/a
29	MYC	chr11:48041543-48042487	NB4	blood:	n/a	chr11:48042327-48042337
30	FOS	chr11:48041679-48042050	MCF10A-Er-Src	breast:	n/a	n/a
31	STAT5A	chr11:48040136-48042222	GM12878	blood:	n/a	chr11:48040714-48040722
32	ATF2	chr11:48041464-48042090	GM12878	blood:	n/a	n/a
33	TCF12	chr11:48041702-48042028	GM12878	blood:	n/a	n/a
34	CTCF	chr11:48041759-48041844	Lung_OC	lung:	n/a	n/a
35	POLR2A	chr11:48040915-48042413	Raji	blood:	n/a	n/a
36	BATF	chr11:48041683-48042086	GM12878	blood:	n/a	chr11:48041720-48041728
37	CTCF	chr11:48041745-48041882	HUVEC	blood vessel:	n/a	n/a
38	CTCF	chr11:48041750-48041873	Spleen_OC	spleen:	n/a	n/a
39	CTCF	chr11:48041700-48041850	GM12868	blood:	n/a	n/a
40	EBF1	chr11:48041637-48042351	GM12878	blood:	n/a	n/a
41	CTCF	chr11:48041718-48041900	GM12878	blood:	n/a	n/a
42	SPI1	chr11:48041604-48042110	HL-60	blood:	n/a	n/a
43	IRF4	chr11:48041559-48042185	GM12878	blood:	n/a	n/a
44	CTCF	chr11:48041793-48041826	GM10266	blood:	n/a	n/a
45	CTCF	chr11:48041619-48042013	GM12878	blood:	n/a	n/a
46	FOXM1	chr11:48041487-48042218	GM12878	blood:	n/a	n/a
47	SPI1	chr11:48041545-48042278	HL-60	blood:	n/a	n/a
48	EBF1	chr11:48041664-48042018	GM12878	blood:	n/a	n/a
49	RAD21	chr11:48041568-48041956	GM12878	blood:	n/a	n/a
50	FOXM1	chr11:48040730-48042218	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:48041783-48041833	SKMC	muscle:	n/a
2	chr11:48041783-48041833	Jurkat	blood:	n/a
3	chr11:48041783-48041833	LNCaP	prostate:	n/a
4	chr11:48041783-48041833	RPTEC	kidney:	n/a
5	chr11:48041783-48041833	ovcar-3	ovarian:	n/a
6	chr11:48041783-48041833	NT2-D1	testis:	n/a
7	chr11:48041783-48041833	U87	brain:	n/a
8	chr11:48041783-48041833	A549	lung:	n/a
9	chr11:48041783-48041833	HCT-116	colon:	n/a
10	chr11:48041783-48041833	HRCEpiC	kidney:	n/a
11	chr11:48041783-48041833	SAEC	small airway:	n/a
12	chr11:48041783-48041833	HPAEpiC	pulmonary alveolar:	n/a
13	chr11:48041783-48041833	MCF-7	breast:	n/a
14	chr11:48041783-48041833	CMK	blood:	n/a
15	chr11:48041783-48041833	AoSMC	blood vessel:	n/a
16	chr11:48041783-48041833	PrEC	prostate:	n/a
17	chr11:48041783-48041833	HepG2	liver:	n/a
18	chr11:48041783-48041833	GM19239	blood:	n/a
19	chr11:48041783-48041833	AG04449	skin:	fetal
20	chr11:48041783-48041833	HEK293	kidney:	embryo
21	chr11:48041783-48041833	AG09319	gingival:	n/a
22	chr11:48041783-48041833	HUVEC	blood vessel:	n/a
23	chr11:48041783-48041833	ECC-1	luminal epithelium:	n/a
24	chr11:48041783-48041833	HAEpiC	amniotic membrane:	n/a
25	chr11:48041783-48041833	GM12891	blood:	n/a
26	chr11:48041783-48041833	Hepatocyte	liver:	n/a
27	chr11:48041783-48041833	HMEC	breast:	n/a
28	chr11:48041783-48041833	GM12878	blood:	n/a
29	chr11:48041783-48041833	NH-A	brain:	n/a
30	chr11:48041783-48041833	Hela-S3	cervix:	n/a
31	chr11:48041783-48041833	Caco-2	colon:	n/a
32	chr11:48041783-48041833	HL-60	blood:	n/a
33	chr11:48041783-48041833	HEEpiC	esophagus:	n/a
34	chr11:48041783-48041833	GM06990	blood:	n/a
35	chr11:48041783-48041833	HCF	heart:	n/a
36	chr11:48041783-48041833	HCM	heart:	n/a
37	chr11:48041783-48041833	AG10803	skin:	n/a
38	chr11:48041783-48041833	HNPCEpiC	eye:	n/a
39	chr11:48041783-48041833	SK-N-SH	brain:	n/a
40	chr11:48041783-48041833	AG04450	lung:	fetal
41	chr11:48041783-48041833	NB4	blood:	n/a
42	chr11:48041783-48041833	NHDF-neo	bronchial:	n/a
43	chr11:48041783-48041833	T-47D	breast:	n/a
44	chr11:48041783-48041833	HIPEpiC	eye:	n/a
45	chr11:48041783-48041833	PFSK-1	brain:	n/a
46	chr11:48041783-48041833	SK-N-MC	brain:	n/a
47	chr11:48041783-48041833	GM12892	blood:	n/a
48	chr11:48041783-48041833	MCF10A-Er-Src	breast:	n/a
49	chr11:48041783-48041833	NHBE	bronchial:	n/a
50	chr11:48041783-48041833	K562	blood:	n/a

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

Variant related genes	Relation type
ENSG00000254879	TF binding region
ENSG00000254879	CpG island

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11039489	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11039492	1.00[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[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs11822835	1.00[AMR][1000 genomes]
rs11825374	1.00[AMR][1000 genomes]
rs12272204	1.00[YRI][hapmap]
rs12272622	1.00[AMR][1000 genomes]
rs12275069	1.00[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]
rs1228027	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[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12282960	1.00[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]
rs12292463	1.00[YRI][hapmap]
rs12293503	1.00[YRI][hapmap]
rs12294321	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12294477	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12295345	1.00[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[YRI][hapmap];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]
rs4752870	1.00[MKK][hapmap]
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[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];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:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48018800-48042000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr11:48025000-48045200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr11:48027400-48044000	Enhancers	Primary T cells fromperipheralblood	blood
4	chr11:48032400-48042600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr11:48032400-48045200	Enhancers	Primary B cells from peripheral blood	blood
6	chr11:48032600-48042800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr11:48032800-48042400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr11:48035400-48046200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:48035600-48053000	Weak transcription	Thymus	Thymus
10	chr11:48035600-48056600	Weak transcription	HSMM	muscle
11	chr11:48035800-48042000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:48037400-48045200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr11:48037600-48042400	Enhancers	Brain Substantia Nigra	brain
14	chr11:48037800-48046400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:48038000-48052400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:48038600-48042400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:48038600-48042400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr11:48038800-48042200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:48038800-48042600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:48038800-48042600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr11:48038800-48045000	Enhancers	Primary hematopoietic stem cells	blood
22	chr11:48039000-48042200	Enhancers	Liver	Liver
23	chr11:48039000-48042600	Flanking Active TSS	GM12878-XiMat	blood
24	chr11:48039200-48042400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:48039400-48042000	Enhancers	HUVEC	blood vessel
26	chr11:48039400-48042200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:48039400-48042600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr11:48039600-48042800	Enhancers	Stomach Mucosa	stomach
29	chr11:48039600-48046000	Weak transcription	Hela-S3	cervix
30	chr11:48039800-48042400	Enhancers	Placenta	Placenta
31	chr11:48040000-48042400	Enhancers	Adipose Nuclei	Adipose
32	chr11:48040000-48046400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr11:48040000-48050600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr11:48040000-48050800	Weak transcription	Osteobl	bone
35	chr11:48040200-48046200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr11:48040400-48041800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:48040400-48041800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr11:48040400-48042000	Weak transcription	Colonic Mucosa	Colon
39	chr11:48040400-48043600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr11:48040600-48042000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr11:48040600-48042400	Enhancers	Brain Anterior Caudate	brain
42	chr11:48040600-48047200	Weak transcription	Right Ventricle	heart
43	chr11:48040600-48053200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr11:48040800-48041800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:48040800-48041800	Weak transcription	Brain Angular Gyrus	brain
46	chr11:48040800-48041800	Enhancers	Fetal Intestine Small	intestine
47	chr11:48040800-48041800	Weak transcription	Lung	lung
48	chr11:48040800-48041800	Weak transcription	Pancreas	Pancrea
49	chr11:48040800-48041800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr11:48040800-48042000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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