Variant report

Variant	rs12490048
Chromosome Location	chr3:113339041-113339042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113331903..113333540-chr3:113337215..113339605,2	MCF-7	breast:
2	chr3:113323890..113330081-chr3:113337547..113341799,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000072858	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10934239	0.81[AMR][1000 genomes]
rs10934240	0.81[AMR][1000 genomes]
rs11914863	0.86[AMR][1000 genomes]
rs11918910	0.86[AMR][1000 genomes]
rs11920913	0.81[AMR][1000 genomes]
rs11921407	0.86[AMR][1000 genomes]
rs12486414	0.93[AMR][1000 genomes]
rs12489192	0.93[AMR][1000 genomes]
rs12490651	0.93[AMR][1000 genomes]
rs12491540	0.93[AMR][1000 genomes]
rs12492290	0.93[AMR][1000 genomes]
rs12492542	0.93[AMR][1000 genomes]
rs12492783	1.00[AMR][1000 genomes]
rs12493602	0.93[AMR][1000 genomes]
rs12493935	0.81[AMR][1000 genomes]
rs12494777	0.93[AMR][1000 genomes]
rs12495298	0.86[AMR][1000 genomes]
rs12495713	0.93[AMR][1000 genomes]
rs12496604	0.93[AMR][1000 genomes]
rs12496617	0.86[AMR][1000 genomes]
rs12497754	0.93[AMR][1000 genomes]
rs16861230	1.00[AMR][1000 genomes]
rs16861233	1.00[AMR][1000 genomes]
rs16861235	1.00[AMR][1000 genomes]
rs16861331	0.93[AMR][1000 genomes]
rs2292512	1.00[AMR][1000 genomes]
rs2566972	0.81[AMR][1000 genomes]
rs2603791	0.81[AMR][1000 genomes]
rs3773686	1.00[AMR][1000 genomes]
rs57010522	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS 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	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers 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 miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113285200-113343400	Weak transcription	Small Intestine	intestine
2	chr3:113320400-113345600	Weak transcription	Fetal Intestine Small	intestine
3	chr3:113320800-113347600	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr3:113321200-113349200	Weak transcription	Brain Angular Gyrus	brain
5	chr3:113321200-113349600	Weak transcription	Lung	lung
6	chr3:113322600-113348600	Weak transcription	Colonic Mucosa	Colon
7	chr3:113323200-113342400	Weak transcription	Pancreas	Pancrea
8	chr3:113326200-113340000	Weak transcription	Fetal Stomach	stomach
9	chr3:113326200-113340600	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr3:113326600-113340600	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr3:113326600-113350000	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:113326800-113340400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:113326800-113344800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:113326800-113349200	Strong transcription	GM12878-XiMat	blood
15	chr3:113326800-113350200	Strong transcription	Primary T cells from cord blood	blood
16	chr3:113327400-113339200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:113327400-113340400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:113331400-113345400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:113332200-113342600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:113332400-113346600	Weak transcription	Gastric	stomach
21	chr3:113332400-113349200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:113332600-113342200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr3:113333600-113340600	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:113333600-113352000	Weak transcription	Spleen	Spleen
25	chr3:113334600-113349400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:113335200-113339800	Weak transcription	Fetal Thymus	thymus
27	chr3:113335200-113341600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:113335400-113339400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:113335400-113339600	Weak transcription	Thymus	Thymus
30	chr3:113335400-113344800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:113336400-113350000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:113336400-113350000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:113337000-113344800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:113337600-113343000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:113338000-113340000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:113338000-113340400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:113338400-113339600	Enhancers	Primary B cells from cord blood	blood
38	chr3:113338400-113339600	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr3:113338400-113340000	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr3:113338400-113341000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr3:113338400-113349200	Weak transcription	Esophagus	oesophagus
42	chr3:113338400-113353800	Weak transcription	Stomach Mucosa	stomach
43	chr3:113338600-113339200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:113338600-113339600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:113338600-113340000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr3:113338600-113340000	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr3:113339000-113339600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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