Variant report

Variant	rs12099166
Chromosome Location	chr11:48066048-48066049
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	chr11:48064617-48066459	A549	lung:	n/a	n/a

Variant related genes	Relation type
PTPRJ	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10742833	1.00[CEU][hapmap]
rs10742841	0.89[CEU][hapmap]
rs10838790	1.00[JPT][hapmap]
rs12099043	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1228000	1.00[JPT][hapmap]
rs1228018	1.00[JPT][hapmap]
rs1228020	1.00[JPT][hapmap]
rs12290628	1.00[JPT][hapmap]
rs12292056	0.89[CEU][hapmap];1.00[MEX][hapmap]
rs2950888	1.00[JPT][hapmap]
rs4752898	1.00[CEU][hapmap]
rs66468432	0.91[ASN][1000 genomes]
rs67767527	0.91[ASN][1000 genomes]
rs7111419	1.00[JPT][hapmap]
rs7113640	1.00[JPT][hapmap]
rs7130402	0.80[CEU][hapmap]
rs73464806	0.80[ASN][1000 genomes]
rs900699	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs905480	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	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/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS 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	26 gene(s)	inside rSNPs	diseases
5	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
8	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS 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	6 gene(s)	inside rSNPs	diseases
12	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
15	nsv428573	chr11:48032457-48152344	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
16	nsv897328	chr11:48043053-48901553	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv897329	chr11:48052676-48319974	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
18	nsv1048554	chr11:48062861-48388686	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48047400-48073400	Weak transcription	HSMMtube	muscle
2	chr11:48047400-48073800	Weak transcription	Left Ventricle	heart
3	chr11:48050200-48068200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:48050800-48073000	Weak transcription	Esophagus	oesophagus
5	chr11:48051600-48071200	Weak transcription	Fetal Intestine Large	intestine
6	chr11:48051600-48073800	Weak transcription	Aorta	Aorta
7	chr11:48053800-48073400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:48057000-48069800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr11:48058000-48068600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:48058000-48069600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:48058000-48073400	Weak transcription	K562	blood
12	chr11:48058400-48069600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:48058600-48068800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:48058600-48069600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:48058600-48072000	Weak transcription	Fetal Kidney	kidney
16	chr11:48059800-48066800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:48060000-48073000	Weak transcription	Hela-S3	cervix
18	chr11:48060000-48073200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:48061000-48068000	Enhancers	Brain Anterior Caudate	brain
20	chr11:48062000-48067600	Enhancers	Brain Cingulate Gyrus	brain
21	chr11:48062400-48068000	Enhancers	Brain Angular Gyrus	brain
22	chr11:48062600-48066200	Enhancers	Liver	Liver
23	chr11:48062600-48067600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr11:48062600-48073400	Weak transcription	Gastric	stomach
25	chr11:48062800-48070600	Weak transcription	Pancreas	Pancrea
26	chr11:48063000-48068200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr11:48063000-48068200	Enhancers	Primary B cells from peripheral blood	blood
28	chr11:48063200-48067600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr11:48063600-48068200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr11:48063800-48067200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr11:48063800-48067400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:48064000-48066200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:48064000-48066800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr11:48064200-48066400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:48064200-48066600	Enhancers	Primary hematopoietic stem cells	blood
36	chr11:48064200-48067000	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr11:48064200-48068200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr11:48064200-48068800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:48064200-48069000	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr11:48064400-48068600	Enhancers	Brain Substantia Nigra	brain
41	chr11:48064400-48068600	Weak transcription	Stomach Mucosa	stomach
42	chr11:48064400-48069600	Weak transcription	Fetal Stomach	stomach
43	chr11:48064400-48069600	Weak transcription	NHDF-Ad	bronchial
44	chr11:48064400-48073200	Weak transcription	NHLF	lung
45	chr11:48064600-48068000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:48064600-48068200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr11:48064600-48069200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:48064600-48073400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:48064800-48066200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:48064800-48066200	Enhancers	Fetal Thymus	thymus

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