Variant report

Variant	rs4910588
Chromosome Location	chr11:3963675-3963676
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	RUNX3	chr11:3963349-3964266	GM12878	blood:	n/a	n/a
2	RAD21	chr11:3963607-3964227	HepG2	liver:	n/a	n/a
3	MAZ	chr11:3963467-3963997	HepG2	liver:	n/a	n/a
4	RCOR1	chr11:3963662-3964032	K562	blood:	n/a	n/a
5	STAT5A	chr11:3963404-3963853	GM12878	blood:	n/a	n/a
6	SMC3	chr11:3963648-3964328	HepG2	liver:	n/a	chr11:3963812-3963826
7	MYBL2	chr11:3963574-3964247	HepG2	liver:	n/a	n/a
8	RAD21	chr11:3963595-3964060	HepG2	liver:	n/a	n/a
9	RUNX3	chr11:3963319-3964234	GM12878	blood:	n/a	n/a
10	FOXA1	chr11:3963621-3964116	HepG2	liver:	n/a	chr11:3963873-3963888 chr11:3963889-3963904 chr11:3963875-3963887
11	CTCF	chr11:3963644-3963999	K562	blood:	n/a	chr11:3963810-3963828 chr11:3963811-3963827
12	FOXA1	chr11:3963558-3964239	HepG2	liver:	n/a	chr11:3963873-3963888 chr11:3963889-3963904 chr11:3963875-3963887
13	NFIC	chr11:3963419-3964144	GM12878	blood:	n/a	n/a
14	CHD2	chr11:3963662-3963835	HepG2	liver:	n/a	n/a
15	TEAD4	chr11:3963621-3964235	HepG2	liver:	n/a	n/a
16	FOXA2	chr11:3963632-3964271	HepG2	liver:	n/a	chr11:3963875-3963887
17	FOXA1	chr11:3963581-3964180	HepG2	liver:	n/a	chr11:3963873-3963888 chr11:3963889-3963904 chr11:3963875-3963887
18	CTCF	chr11:3963636-3963941	HepG2	liver:	n/a	chr11:3963810-3963828 chr11:3963811-3963827
19	MTA3	chr11:3963442-3964226	GM12878	blood:	n/a	n/a
20	JUND	chr11:3963661-3963937	K562	blood:	n/a	n/a
21	RAD21	chr11:3963535-3964220	HepG2	liver:	n/a	n/a
22	ATF1	chr11:3963575-3963897	K562	blood:	n/a	n/a
23	ARID3A	chr11:3963620-3964681	HepG2	liver:	n/a	n/a
24	FOXA2	chr11:3963150-3964464	HepG2	liver:	n/a	chr11:3963875-3963887
25	RCOR1	chr11:3963514-3964113	HepG2	liver:	n/a	n/a
26	NFIC	chr11:3963610-3964119	HepG2	liver:	n/a	n/a
27	FOXA1	chr11:3963574-3964234	HepG2	liver:	n/a	chr11:3963873-3963888 chr11:3963889-3963904 chr11:3963875-3963887
28	EP300	chr11:3963554-3964230	HepG2	liver:	n/a	chr11:3963878-3963888 chr11:3963588-3963595

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3963150..3965730-chr11:3971154..3972718,2	K562	blood:
2	chr11:3959785..3962625-chr11:3963394..3965455,2	K562	blood:

Variant related genes	Relation type
STIM1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10734400	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10742194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742207	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767775	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10835500	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11030584	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2860454	1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2923946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2923958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2923959	0.82[AFR][1000 genomes]
rs2959058	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2959059	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2959080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4379839	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910881	0.81[YRI][hapmap]
rs6578430	0.80[EUR][1000 genomes]
rs727152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7928763	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	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 Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' 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	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases
6	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv896895	chr11:3942001-3972236	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3950400-3972200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:3951200-3965400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:3951200-3967600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:3954000-3963800	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr11:3956200-3964000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:3958800-3968000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr11:3959600-3963800	Weak transcription	Fetal Lung	lung
8	chr11:3960000-3967600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr11:3960200-3967600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:3961000-3964200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:3961200-3964600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:3961200-4002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:3961400-3964400	Enhancers	Right Atrium	heart
14	chr11:3961400-3964800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:3961400-3965200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr11:3961400-3968600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:3961400-3968600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr11:3961400-3969200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:3961600-3963800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:3961600-3963800	Weak transcription	HMEC	breast
21	chr11:3961600-3966400	Enhancers	NHDF-Ad	bronchial
22	chr11:3961600-3967600	Weak transcription	Brain Angular Gyrus	brain
23	chr11:3961600-3967800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:3961600-3968000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:3961600-3968400	Weak transcription	NHEK	skin
26	chr11:3961600-3975200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:3961800-3963800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr11:3961800-3964000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:3961800-3965600	Weak transcription	NHLF	lung
30	chr11:3961800-3968000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:3962000-3963800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:3962000-3965200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr11:3962000-3971800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:3962000-3973400	Weak transcription	Ovary	ovary
35	chr11:3962400-3964000	Enhancers	Thymus	Thymus
36	chr11:3962400-3968000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr11:3962400-3968400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr11:3962600-3968200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:3963000-3964000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr11:3963000-3964800	Enhancers	Right Ventricle	heart
41	chr11:3963000-3966400	Enhancers	Psoas Muscle	Psoas
42	chr11:3963000-3967000	Enhancers	Fetal Thymus	thymus
43	chr11:3963000-3968600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr11:3963000-3973200	Enhancers	Primary B cells from peripheral blood	blood
45	chr11:3963200-3964400	Flanking Active TSS	GM12878-XiMat	blood
46	chr11:3963200-3964800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr11:3963200-3965400	Enhancers	Liver	Liver
48	chr11:3963200-3967800	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr11:3963200-3968400	Enhancers	Primary hematopoietic stem cells	blood
50	chr11:3963400-3963800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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