Variant report

Variant	rs16929761
Chromosome Location	chr11:3816777-3816778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:3816051-3819517	IMR90	lung:	n/a	n/a
2	POLR2A	chr11:3816253-3820653	PANC-1	pancreas:	n/a	n/a
3	CEBPB	chr11:3816504-3816793	K562	blood:	n/a	chr11:3816626-3816637
4	ZKSCAN1	chr11:3816737-3816935	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr11:3816505-3816792	A549	lung:	n/a	chr11:3816626-3816637
6	POLR2A	chr11:3816677-3816854	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:3816282-3819657	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr11:3816342-3819654	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr11:3816665-3817085	GM12878	blood:	n/a	n/a
10	FOXA2	chr11:3816596-3816895	HepG2	liver:	n/a	n/a
11	FOXA1	chr11:3816574-3816981	HepG2	liver:	n/a	n/a
12	POLR2A	chr11:3816305-3816878	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr11:3816109-3819778	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:3815537..3818080-chr11:3829335..3832010,3	K562	blood:
2	chr11:3816139..3821205-chr11:3826361..3831544,11	MCF-7	breast:
3	chr11:3815253..3816914-chr11:3817016..3818903,2	MCF-7	breast:
4	chr11:3816760..3821195-chr11:3827310..3829330,5	K562	blood:
5	chr11:3815959..3820545-chr11:3854514..3864703,12	K562	blood:
6	chr11:3792691..3794199-chr11:3815236..3817396,2	MCF-7	breast:
7	chr11:3810141..3811927-chr11:3815704..3818583,2	K562	blood:
8	chr11:3816391..3818213-chr11:3846207..3848807,2	K562	blood:
9	chr11:3813727..3817050-chr11:3817081..3819482,4	K562	blood:
10	chr11:3816345..3819166-chr11:3875729..3878020,2	K562	blood:

No data

Variant related genes	Relation type
PGAP2	TF binding region
ENSG00000177105	Chromatin interaction
ENSG00000229368	Chromatin interaction
ENSG00000263421	Chromatin interaction
ENSG00000110713	Chromatin interaction
ENSG00000228661	Chromatin interaction
ENSG00000167323	Chromatin interaction
ENSG00000148985	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16929738	1.00[AMR][1000 genomes]
rs17173880	1.00[AMR][1000 genomes]
rs34160712	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55726541	1.00[AMR][1000 genomes]
rs7126968	1.00[AMR][1000 genomes]
rs74050208	1.00[AMR][1000 genomes]
rs74050302	1.00[AMR][1000 genomes]
rs74053503	1.00[AMR][1000 genomes]
rs7937476	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7941740	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9666326	1.00[AMR][1000 genomes]
rs9666327	1.00[AMR][1000 genomes]
rs9666328	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	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
7	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3739400-3817600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:3780600-3817000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:3793800-3816800	Weak transcription	Fetal Heart	heart
4	chr11:3793800-3817000	Weak transcription	Fetal Brain Male	brain
5	chr11:3800400-3817000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr11:3800400-3817600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:3800600-3817000	Weak transcription	HSMMtube	muscle
8	chr11:3800600-3817200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr11:3808800-3816800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:3808800-3817000	Weak transcription	NHDF-Ad	bronchial
11	chr11:3809000-3817200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:3810800-3816800	Strong transcription	Fetal Intestine Small	intestine
13	chr11:3811200-3816800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:3811200-3816800	Strong transcription	Fetal Intestine Large	intestine
15	chr11:3811200-3817000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:3813400-3817000	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr11:3813600-3817000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:3814000-3816800	Weak transcription	Fetal Kidney	kidney
19	chr11:3814200-3816800	Genic enhancers	Left Ventricle	heart
20	chr11:3814800-3816800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:3814800-3816800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr11:3814800-3817000	Weak transcription	Brain Substantia Nigra	brain
23	chr11:3814800-3817000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:3815000-3817000	Weak transcription	NH-A	brain
25	chr11:3815000-3817200	Weak transcription	Aorta	Aorta
26	chr11:3815000-3817400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr11:3815000-3817600	Weak transcription	Spleen	Spleen
28	chr11:3815000-3817800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:3815200-3817000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr11:3815200-3817600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr11:3815200-3817600	Weak transcription	Pancreas	Pancrea
32	chr11:3815400-3816800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr11:3815400-3816800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr11:3815400-3816800	Enhancers	HepG2	liver
35	chr11:3815600-3816800	Enhancers	Right Ventricle	heart
36	chr11:3815600-3817000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
37	chr11:3815600-3817200	Weak transcription	Fetal Muscle Leg	muscle
38	chr11:3815800-3816800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:3815800-3816800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:3815800-3816800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr11:3815800-3817000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr11:3815800-3817200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr11:3815800-3817200	Enhancers	Brain Angular Gyrus	brain
44	chr11:3815800-3817400	Enhancers	Primary B cells from peripheral blood	blood
45	chr11:3816000-3816800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
46	chr11:3816000-3816800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr11:3816000-3816800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:3816000-3816800	Enhancers	Adipose Nuclei	Adipose
49	chr11:3816000-3817000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr11:3816000-3817000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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