Variant report

Variant	rs28406816
Chromosome Location	chr11:33048154-33048155
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:33038166..33041060-chr11:33046643..33049387,2	MCF-7	breast:
2	chr11:33047529..33049150-chr11:33058361..33061018,2	MCF-7	breast:
3	chr11:33037810..33039404-chr11:33046604..33049179,2	K562	blood:
4	chr11:33040431..33043314-chr11:33047289..33049543,3	K562	blood:
5	chr11:33043473..33045913-chr11:33047452..33049632,3	K562	blood:
6	chr11:33043183..33045594-chr11:33046266..33049632,4	K562	blood:

Variant related genes	Relation type
ENSG00000176148	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10430851	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10767981	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032141	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2273539	0.82[ASN][1000 genomes]
rs4261257	0.81[AMR][1000 genomes]
rs4275605	0.81[EUR][1000 genomes]
rs4382878	0.86[EUR][1000 genomes]
rs4561187	0.96[EUR][1000 genomes]
rs7108667	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7121724	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129799	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72901275	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72901281	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758262	chr11:32714643-33049940	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759815	chr11:32714643-33049940	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	esv2753057	chr11:32796124-33061724	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	esv2753743	chr11:32796124-33084924	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv1040484	chr11:32951066-33093204	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1046198	chr11:32954100-33075142	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv2762904	chr11:32969258-33586535	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
8	nsv1041149	chr11:32981164-33496670	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv1053823	chr11:32981164-33533356	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv897194	chr11:32993887-33471804	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
11	nsv1040572	chr11:33008191-33518964	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
12	nsv540989	chr11:33008191-33518964	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
13	nsv1042860	chr11:33008191-33562490	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
14	nsv540990	chr11:33008191-33562490	Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
15	nsv533840	chr11:33008192-33595324	Bivalent Enhancer Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
16	nsv1051521	chr11:33008435-33239765	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
17	nsv540991	chr11:33008435-33239765	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
18	nsv1044478	chr11:33008435-33656273	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
19	nsv897195	chr11:33012493-33559186	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
20	nsv1053344	chr11:33028973-33499346	Bivalent Enhancer Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
21	nsv1046243	chr11:33043155-33439216	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
22	nsv540992	chr11:33043155-33439216	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
23	nsv1050944	chr11:33043155-33656273	Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
24	nsv540993	chr11:33043155-33656273	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28406816	LOC283267	Cis_1M	lymphoblastoid	RTeQTL
rs28406816	PIGCP1	cis	Skin Sun Exposed Lower leg	GTEx
rs28406816	PIGCP1	cis	Artery Tibial	GTEx
rs28406816	TCP11L1	Cis_1M	lymphoblastoid	RTeQTL
rs28406816	TCP11L1	cis	Artery Tibial	GTEx
rs28406816	TCP11L1	cis	Whole Blood	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33038200-33060200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:33038800-33049800	Weak transcription	HMEC	breast
3	chr11:33039200-33048400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:33039200-33053800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:33039200-33060200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr11:33039400-33048400	Weak transcription	NHDF-Ad	bronchial
7	chr11:33039400-33049800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:33039400-33050000	Weak transcription	Brain Angular Gyrus	brain
9	chr11:33039400-33060400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:33039600-33060400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:33040200-33048400	Weak transcription	NHEK	skin
12	chr11:33040800-33049400	Weak transcription	Psoas Muscle	Psoas
13	chr11:33040800-33060200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr11:33040800-33060400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr11:33041000-33052400	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:33041400-33060200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr11:33043400-33049600	Weak transcription	HSMMtube	muscle
18	chr11:33043400-33049800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:33043600-33048600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:33043600-33060200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:33043800-33048600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr11:33043800-33049600	Weak transcription	Fetal Lung	lung
23	chr11:33043800-33052400	Weak transcription	Hela-S3	cervix
24	chr11:33043800-33056600	Weak transcription	A549	lung
25	chr11:33044000-33048600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr11:33044000-33048600	Weak transcription	Osteobl	bone
27	chr11:33044000-33049600	Weak transcription	HepG2	liver
28	chr11:33044400-33050000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr11:33044400-33056800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr11:33045200-33056800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:33045200-33060600	Weak transcription	Small Intestine	intestine
32	chr11:33045800-33058400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr11:33046000-33057000	Strong transcription	HSMM	muscle
34	chr11:33046200-33048200	Weak transcription	Fetal Intestine Large	intestine
35	chr11:33046800-33048200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:33046800-33048400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:33046800-33048400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:33046800-33049600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr11:33046800-33050200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:33046800-33051000	Weak transcription	Ovary	ovary
41	chr11:33046800-33054000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:33047000-33048800	Weak transcription	Fetal Intestine Small	intestine
43	chr11:33047000-33049600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:33047000-33060400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:33047000-33060600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr11:33047200-33049600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr11:33047400-33048200	Strong transcription	K562	blood
48	chr11:33047400-33048800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr11:33047600-33048600	Weak transcription	Brain Hippocampus Middle	brain
50	chr11:33048000-33048200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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