Variant report

Variant	rs12099352
Chromosome Location	chr11:85410591-85410592
allele	C/T
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	POLR2A	chr11:85410487-85410630	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:85409414..85413746-chr11:85414065..85417765,4	K562	blood:
2	chr11:85405165..85408368-chr11:85410151..85413068,4	MCF-7	breast:
3	chr11:85406392..85407913-chr11:85410539..85412560,2	K562	blood:

Variant related genes	Relation type
SYTL2	TF binding region
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17148332	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17148370	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17148398	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17148484	1.00[AMR][1000 genomes]
rs3168151	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4570600	1.00[AMR][1000 genomes]
rs55951903	1.00[AMR][1000 genomes]
rs6592249	1.00[AMR][1000 genomes]
rs6592261	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73502601	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73518849	1.00[AMR][1000 genomes]
rs7931532	1.00[AMR][1000 genomes]
rs7946536	0.98[AFR][1000 genomes];1.00[AMR][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	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' 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
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription 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	56 gene(s)	inside rSNPs	diseases
5	nsv468768	chr11:85395180-85436352	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv555632	chr11:85395180-85436352	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv898050	chr11:85406915-85499290	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85394000-85427400	Weak transcription	Small Intestine	intestine
2	chr11:85394200-85410600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr11:85394200-85410800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:85394400-85410600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr11:85396800-85429800	Weak transcription	Stomach Mucosa	stomach
6	chr11:85397000-85412600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:85397000-85417400	Weak transcription	Gastric	stomach
8	chr11:85397000-85418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:85397000-85425400	Weak transcription	Lung	lung
10	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
11	chr11:85397600-85422000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:85397600-85428400	Weak transcription	Brain Angular Gyrus	brain
13	chr11:85397800-85410600	Weak transcription	Fetal Intestine Small	intestine
14	chr11:85397800-85412400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:85397800-85421600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:85397800-85430000	Weak transcription	Ovary	ovary
17	chr11:85398000-85427600	Weak transcription	Brain Substantia Nigra	brain
18	chr11:85398400-85413000	Weak transcription	Fetal Stomach	stomach
19	chr11:85400000-85410600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:85400400-85411400	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr11:85401200-85410600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr11:85404800-85410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr11:85405000-85418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:85406000-85410600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr11:85406200-85429800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:85406400-85413800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr11:85406600-85416000	Weak transcription	A549	lung
28	chr11:85406600-85416800	Weak transcription	NH-A	brain
29	chr11:85406800-85416000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:85407000-85416400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:85407200-85416200	Strong transcription	HSMM	muscle
32	chr11:85407400-85413000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:85407600-85410600	Weak transcription	Fetal Muscle Leg	muscle
34	chr11:85408200-85410800	Weak transcription	Fetal Kidney	kidney
35	chr11:85408200-85412400	Weak transcription	Brain Hippocampus Middle	brain
36	chr11:85408600-85426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr11:85409000-85410600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr11:85409000-85410600	Weak transcription	GM12878-XiMat	blood
39	chr11:85409000-85421800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:85409000-85425200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:85409200-85410800	Weak transcription	HSMMtube	muscle
42	chr11:85409200-85413400	Weak transcription	NHLF	lung
43	chr11:85409400-85410600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr11:85409400-85410800	Weak transcription	Primary T cells from cord blood	blood
45	chr11:85409400-85418200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:85409400-85427200	Weak transcription	Fetal Lung	lung
47	chr11:85409800-85411400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:85409800-85412400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr11:85410000-85413000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr11:85410200-85413000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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