Variant report

Variant	rs11826413
Chromosome Location	chr11:85417319-85417320
allele	C/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	GATA3	chr11:85416682-85417577	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr11:85416912-85417875	MCF-7	breast:	n/a	n/a
3	TCF12	chr11:85416624-85417533	SK-N-SH	brain:	n/a	n/a
4	JUND	chr11:85416828-85417438	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr11:85416744-85417494	SK-N-SH	brain:	n/a	n/a
6	FOSL2	chr11:85416803-85417383	SK-N-SH	brain:	n/a	n/a
7	JUND	chr11:85416748-85417426	SK-N-SH	brain:	n/a	n/a
8	MAFK	chr11:85417258-85417366	HepG2	liver:	n/a	n/a
9	MEF2A	chr11:85416673-85417433	SK-N-SH	brain:	n/a	chr11:85416735-85416750 chr11:85417051-85417060 chr11:85416734-85416750 chr11:85417048-85417063 chr11:85416736-85416747 chr11:85416734-85416749 chr11:85416735-85416749 chr11:85417047-85417063 chr11:85417046-85417067 chr11:85416730-85416751 chr11:85417049-85417060 chr11:85416730-85416751 chr11:85416735-85416750 chr11:85416737-85416746
10	PBX3	chr11:85416786-85417542	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr11:85416708-85417412	SK-N-SH	brain:	n/a	n/a
12	EP300	chr11:85416684-85417564	SK-N-SH	brain:	n/a	n/a
13	PBX3	chr11:85416832-85417463	SK-N-SH	brain:	n/a	n/a
14	NFIC	chr11:85416670-85417436	SK-N-SH	brain:	n/a	n/a
15	MAFK	chr11:85417192-85417466	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:85407594..85410052-chr11:85416744..85418480,2	K562	blood:
2	chr11:85374847..85376948-chr11:85415387..85418277,3	K562	blood:
3	chr11:85409414..85413746-chr11:85414065..85417765,4	K562	blood:

Variant related genes	Relation type
SYTL2	TF binding region
ENSG00000137504	Chromatin interaction
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10501596	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs11822544	1.00[EUR][1000 genomes]
rs11827081	1.00[EUR][1000 genomes]
rs11828165	1.00[EUR][1000 genomes]
rs12099248	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs12099426	1.00[EUR][1000 genomes]
rs1445515	1.00[EUR][1000 genomes]
rs17148301	0.82[YRI][hapmap]
rs17148334	0.82[YRI][hapmap]
rs17148344	0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17148395	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs17148401	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs17148417	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs17148419	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs17148431	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs17148438	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs17148453	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs17148464	1.00[EUR][1000 genomes]
rs17148473	1.00[EUR][1000 genomes]
rs17148488	1.00[EUR][1000 genomes]
rs17148584	1.00[EUR][1000 genomes]
rs28450318	1.00[EUR][1000 genomes]
rs34050255	1.00[EUR][1000 genomes]
rs35177514	1.00[EUR][1000 genomes]
rs3851177	1.00[EUR][1000 genomes]
rs4088048	1.00[EUR][1000 genomes]
rs55739500	1.00[EUR][1000 genomes]
rs56386215	1.00[EUR][1000 genomes]
rs57373902	1.00[EUR][1000 genomes]
rs58519079	1.00[EUR][1000 genomes]
rs60068371	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60389124	1.00[EUR][1000 genomes]
rs60958929	1.00[EUR][1000 genomes]
rs7111778	0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs7115189	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs7116307	0.82[YRI][hapmap]
rs7119154	1.00[EUR][1000 genomes]
rs7124851	0.90[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7129079	1.00[EUR][1000 genomes]
rs73502585	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73519658	1.00[EUR][1000 genomes]
rs73519686	1.00[EUR][1000 genomes]
rs7925247	1.00[EUR][1000 genomes]
rs7928873	1.00[EUR][1000 genomes]
rs7938187	1.00[EUR][1000 genomes]
rs7946866	0.91[YRI][hapmap];1.00[EUR][1000 genomes]
rs7950767	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9943496	0.82[YRI][hapmap]

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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85394000-85427400	Weak transcription	Small Intestine	intestine
2	chr11:85396800-85429800	Weak transcription	Stomach Mucosa	stomach
3	chr11:85397000-85417400	Weak transcription	Gastric	stomach
4	chr11:85397000-85418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:85397000-85425400	Weak transcription	Lung	lung
6	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
7	chr11:85397600-85422000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:85397600-85428400	Weak transcription	Brain Angular Gyrus	brain
9	chr11:85397800-85421600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:85397800-85430000	Weak transcription	Ovary	ovary
11	chr11:85398000-85427600	Weak transcription	Brain Substantia Nigra	brain
12	chr11:85405000-85418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:85406200-85429800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:85408600-85426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:85409000-85421800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:85409000-85425200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:85409400-85418200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:85409400-85427200	Weak transcription	Fetal Lung	lung
19	chr11:85410600-85424400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr11:85411000-85417400	Weak transcription	Fetal Muscle Leg	muscle
21	chr11:85411800-85424800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr11:85412000-85417400	Weak transcription	Primary T cells from cord blood	blood
23	chr11:85412000-85436800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr11:85412000-85438000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr11:85412600-85427000	Weak transcription	Fetal Intestine Small	intestine
26	chr11:85413600-85427200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:85413600-85429600	Weak transcription	Fetal Stomach	stomach
28	chr11:85413800-85417400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr11:85413800-85417600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:85413800-85418200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:85413800-85430000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr11:85416000-85417600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:85416200-85417800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:85416200-85417800	Genic enhancers	HSMM	muscle
35	chr11:85416400-85417400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:85416400-85417400	Enhancers	HSMMtube	muscle
37	chr11:85416400-85417600	Enhancers	Osteobl	bone
38	chr11:85416600-85417400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr11:85416800-85418600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:85417000-85417400	Weak transcription	NH-A	brain
41	chr11:85417000-85417800	Genic enhancers	NHDF-Ad	bronchial
42	chr11:85417000-85417800	Genic enhancers	NHLF	lung
43	chr11:85417200-85417600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:85417200-85418600	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr11:85417200-85421200	Weak transcription	A549	lung

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