Variant report

Variant	rs58280987
Chromosome Location	chr12:48122814-48122815
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:48122008-48123536	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48121475..48125710-chr12:48127578..48130124,5	MCF-7	breast:
2	chr12:48120779..48123023-chr12:48151598..48154516,2	MCF-7	breast:
3	chr12:48121602..48124147-chr12:48377989..48379947,2	MCF-7	breast:
4	chr12:48121380..48124034-chr12:48159649..48162276,2	MCF-7	breast:
5	chr12:48111396..48114011-chr12:48121790..48123527,2	MCF-7	breast:
6	chr12:48119917..48122886-chr12:48172131..48173866,2	K562	blood:
7	chr12:48122622..48126569-chr12:48133427..48136331,4	K562	blood:
8	chr12:48116837..48120183-chr12:48121904..48124076,4	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ENDOU-1	chr12:48122105-48124381	NONHSAT027937

No data

Variant related genes	Relation type
ENDOU	TF binding region
ENSG00000111405	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1859256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57162394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57691959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58232701	1.00[AFR][1000 genomes]
rs58237186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58348653	1.00[AMR][1000 genomes]
rs58350284	1.00[AMR][1000 genomes]
rs58636268	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59421933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60045275	1.00[AMR][1000 genomes]
rs60186089	0.86[AFR][1000 genomes]
rs60608560	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61033936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61288073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61327127	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61446607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61734364	1.00[AMR][1000 genomes]
rs61739888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7300107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7308032	0.94[AFR][1000 genomes]
rs7314320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300649	1.00[AMR][1000 genomes]
rs73300689	1.00[AMR][1000 genomes]
rs73300701	1.00[AMR][1000 genomes]
rs73302603	1.00[AMR][1000 genomes]
rs73302628	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302698	0.92[AFR][1000 genomes]
rs757283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7965816	1.00[AMR][1000 genomes]
rs877196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs877197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs877198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs879177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs879178	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs879179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9738787	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	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
6	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
7	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48102800-48125000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr12:48111400-48124000	Weak transcription	Gastric	stomach
3	chr12:48112000-48123000	Weak transcription	Pancreas	Pancrea
4	chr12:48112000-48126800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:48112200-48125400	Weak transcription	Fetal Thymus	thymus
6	chr12:48112200-48127000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:48112600-48128600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:48113000-48123400	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:48114000-48134400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:48114200-48132600	Weak transcription	Primary B cells from cord blood	blood
11	chr12:48114600-48128800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:48115200-48126200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:48115600-48123800	Weak transcription	Thymus	Thymus
14	chr12:48115600-48133600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:48115600-48134200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:48115600-48135000	Weak transcription	Primary T cells from cord blood	blood
17	chr12:48116000-48123600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:48116200-48124800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr12:48116200-48124800	Enhancers	Placenta	Placenta
20	chr12:48116200-48134000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:48116800-48130200	Weak transcription	Aorta	Aorta
22	chr12:48117000-48123800	Weak transcription	Lung	lung
23	chr12:48117000-48129000	Weak transcription	Psoas Muscle	Psoas
24	chr12:48117800-48123000	Weak transcription	Liver	Liver
25	chr12:48118200-48128800	Weak transcription	Fetal Intestine Small	intestine
26	chr12:48119000-48126000	Enhancers	NHDF-Ad	bronchial
27	chr12:48119200-48125000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:48119400-48123200	Weak transcription	Left Ventricle	heart
29	chr12:48119400-48123200	Weak transcription	Right Ventricle	heart
30	chr12:48119400-48123400	Weak transcription	Stomach Mucosa	stomach
31	chr12:48119400-48124600	Enhancers	Brain Substantia Nigra	brain
32	chr12:48119600-48125000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr12:48119800-48123000	Enhancers	Brain Cingulate Gyrus	brain
34	chr12:48119800-48123200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:48119800-48123200	Weak transcription	HMEC	breast
36	chr12:48119800-48123200	Weak transcription	K562	blood
37	chr12:48119800-48128600	Weak transcription	Colonic Mucosa	Colon
38	chr12:48120200-48123000	Weak transcription	HSMMtube	muscle
39	chr12:48120200-48123800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:48120200-48123800	Weak transcription	Fetal Lung	lung
41	chr12:48120400-48123000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:48120400-48128600	Weak transcription	NH-A	brain
43	chr12:48120600-48123400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:48120600-48124000	Weak transcription	Right Atrium	heart
45	chr12:48120800-48123800	Enhancers	Brain Hippocampus Middle	brain
46	chr12:48121000-48123200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:48121200-48123200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:48121400-48125800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr12:48122200-48123000	Enhancers	Spleen	Spleen
50	chr12:48122400-48123800	Weak transcription	NHEK	skin

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