Variant report

Variant	rs12290628
Chromosome Location	chr11:47965362-47965363
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47931798..47934604-chr11:47964114..47966502,2	K562	blood:
2	chr11:47964794..47968609-chr11:48000698..48003518,3	MCF-7	breast:
3	chr11:47882484..47885060-chr11:47964831..47967242,2	K562	blood:
4	chr11:47660831..47663188-chr11:47962801..47965480,2	K562	blood:
5	chr11:47964249..47967260-chr11:47967441..47970649,3	K562	blood:
6	chr11:47964759..47967260-chr11:47968299..47969907,3	K562	blood:
7	chr11:47964394..47966332-chr11:47982936..47984660,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149177	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10769307	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838790	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039473	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039480	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12099166	1.00[JPT][hapmap]
rs12270546	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12272781	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12273589	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227997	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1227998	0.80[EUR][1000 genomes]
rs1227999	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228000	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228002	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228004	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1228008	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228018	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1228019	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228020	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228021	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228022	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228023	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12294218	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12295364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681604	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1681627	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681631	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1681637	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1729281	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1729294	0.95[EUR][1000 genomes]
rs1729297	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2626567	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697810	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2930188	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930189	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930195	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2950888	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4752883	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752886	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6485797	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7104376	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7111419	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7113640	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7116080	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119280	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73462871	0.88[ASN][1000 genomes]
rs73462874	0.88[ASN][1000 genomes]
rs73462875	0.88[ASN][1000 genomes]
rs7928153	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932759	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7941441	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs900699	1.00[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47950800-47971800	Weak transcription	Fetal Thymus	thymus
2	chr11:47954400-47968200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr11:47956800-47970200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:47959800-47968800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:47960000-47965400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:47960000-47966000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:47960000-47967600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:47960000-47967800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:47960000-47967800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:47960000-47972400	Weak transcription	Lung	lung
11	chr11:47960800-47965800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:47961200-47965600	Weak transcription	NH-A	brain
13	chr11:47961400-47965600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:47961400-47965600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:47961400-47965600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:47961400-47965800	Weak transcription	NHDF-Ad	bronchial
17	chr11:47961400-47965800	Weak transcription	NHLF	lung
18	chr11:47961400-47965800	Weak transcription	Osteobl	bone
19	chr11:47961800-47965600	Weak transcription	HUVEC	blood vessel
20	chr11:47963000-47965800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:47963200-47965800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:47963400-47965400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:47963800-47965600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:47964000-47965400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr11:47964000-47965400	Weak transcription	K562	blood
26	chr11:47964000-47965600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:47964000-47965600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:47964000-47965600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:47964000-47965600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr11:47964000-47965600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr11:47964000-47965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr11:47964000-47965800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:47964000-47968400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr11:47964000-47968400	Weak transcription	GM12878-XiMat	blood
35	chr11:47964000-47972200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:47964200-47965400	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr11:47964200-47965600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:47964200-47965600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:47964200-47965600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr11:47964200-47968400	Weak transcription	Placenta	Placenta
41	chr11:47964400-47965400	Weak transcription	A549	lung
42	chr11:47964400-47965400	Weak transcription	Hela-S3	cervix
43	chr11:47964400-47967400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr11:47964400-47967400	Weak transcription	Primary B cells from cord blood	blood
45	chr11:47964400-47967400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr11:47964400-47968800	Weak transcription	Right Atrium	heart
47	chr11:47964600-47968600	Weak transcription	Liver	Liver

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