Variant report

Variant	rs11169110
Chromosome Location	chr12:50090616-50090617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50090502..50093036-chr12:50100960..50102656,3	MCF-7	breast:
2	chr12:50080406..50083815-chr12:50089731..50092749,3	MCF-7	breast:
3	chr12:50080143..50085132-chr12:50089232..50093203,6	K562	blood:
4	chr12:50088284..50091215-chr12:50135024..50136697,2	MCF-7	breast:
5	chr12:50086154..50087807-chr12:50089455..50091184,2	MCF-7	breast:
6	chr12:50090084..50092564-chr12:50099997..50102859,2	K562	blood:

Variant related genes	Relation type
ENSG00000161791	Chromatin interaction
ENSG00000139644	Chromatin interaction

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

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

rs_ID	r²[population]
rs10128824	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169114	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169115	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169120	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297814	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299751	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300919	0.83[AFR][1000 genomes]
rs12300962	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12306951	1.00[AMR][1000 genomes]
rs12310580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12312112	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313681	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314036	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12315508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12317162	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12319527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12320895	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1317263	1.00[AMR][1000 genomes]
rs17119738	1.00[AMR][1000 genomes]
rs17123787	1.00[AMR][1000 genomes]
rs17123827	1.00[AMR][1000 genomes]
rs17123879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17123924	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9804867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9805090	0.96[AFR][1000 genomes];1.00[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50078000-50091000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:50078600-50092200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:50078800-50091800	Weak transcription	NH-A	brain
4	chr12:50078800-50092400	Weak transcription	NHLF	lung
5	chr12:50079000-50092000	Weak transcription	Small Intestine	intestine
6	chr12:50079000-50096200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:50079200-50091000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:50079200-50092400	Weak transcription	Fetal Stomach	stomach
9	chr12:50079200-50092800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:50080800-50092800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:50082000-50092800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:50082200-50092000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:50082200-50092800	Weak transcription	Aorta	Aorta
14	chr12:50083400-50092800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:50083600-50092800	Weak transcription	Lung	lung
16	chr12:50083800-50090800	Weak transcription	Brain Substantia Nigra	brain
17	chr12:50083800-50092400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:50084800-50091000	Weak transcription	Right Atrium	heart
19	chr12:50084800-50091800	Weak transcription	K562	blood
20	chr12:50084800-50092000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:50085000-50091000	Weak transcription	Primary B cells from cord blood	blood
22	chr12:50085000-50092000	Weak transcription	Fetal Thymus	thymus
23	chr12:50085000-50092000	Weak transcription	Dnd41	blood
24	chr12:50085000-50092600	Weak transcription	Stomach Mucosa	stomach
25	chr12:50085200-50092000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:50085400-50091200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:50085400-50091200	Weak transcription	Fetal Muscle Leg	muscle
28	chr12:50085400-50092000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr12:50085400-50092800	Weak transcription	Right Ventricle	heart
30	chr12:50085600-50091800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:50086800-50090800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:50086800-50092000	Weak transcription	Brain Angular Gyrus	brain
33	chr12:50088400-50091000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:50088400-50091000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:50088400-50091000	Weak transcription	HSMMtube	muscle
36	chr12:50088400-50091200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:50088400-50091800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:50088400-50091800	Weak transcription	Osteobl	bone
39	chr12:50088400-50092000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr12:50088400-50092200	Weak transcription	NHDF-Ad	bronchial
41	chr12:50088600-50091800	Weak transcription	HSMM	muscle
42	chr12:50088600-50092000	Weak transcription	Placenta	Placenta
43	chr12:50088600-50092200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:50088600-50092400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:50088800-50091200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:50089000-50092000	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr12:50089200-50090800	Enhancers	Primary T cells from cord blood	blood
48	chr12:50089200-50092000	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr12:50089200-50092400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr12:50089200-50093400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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