Variant report

Variant	rs12354466
Chromosome Location	chr10:90789422-90789423
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:90789103..90790276-chr10:90972621..90973980,11	MCF-7	breast:
2	chr10:90789320..90789878-chr10:90977149..90978105,4	MCF-7	breast:
3	chr10:90789343..90790605-chr10:90972311..90973617,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAS-2	chr10:90787438-90793194	NONHSAT015495

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11202933	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202944	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202982	1.00[ASN][1000 genomes]
rs12249543	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355223	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12359678	1.00[ASN][1000 genomes]
rs12360110	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17378695	1.00[ASN][1000 genomes]
rs17449991	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17450261	1.00[ASN][1000 genomes]
rs17450388	1.00[ASN][1000 genomes]
rs1937340	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28562823	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67116800	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67162474	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68099265	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72810915	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72810935	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72810957	1.00[ASN][1000 genomes]
rs72810964	1.00[ASN][1000 genomes]
rs72810969	1.00[ASN][1000 genomes]
rs72812860	1.00[ASN][1000 genomes]
rs73355387	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73365626	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90754000-90789600	Weak transcription	A549	lung
2	chr10:90771600-90789600	Weak transcription	Brain Anterior Caudate	brain
3	chr10:90771800-90808600	Weak transcription	Primary T cells from cord blood	blood
4	chr10:90772400-90795000	Weak transcription	Placenta	Placenta
5	chr10:90772600-90789600	Weak transcription	Fetal Stomach	stomach
6	chr10:90772600-90791800	Weak transcription	Esophagus	oesophagus
7	chr10:90772600-90792000	Weak transcription	Colonic Mucosa	Colon
8	chr10:90772600-90795800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr10:90776600-90792600	Weak transcription	Right Ventricle	heart
10	chr10:90778000-90791200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:90779200-90791600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:90780200-90791400	Weak transcription	Spleen	Spleen
13	chr10:90780400-90789600	Weak transcription	Colon Smooth Muscle	Colon
14	chr10:90780400-90790600	Weak transcription	Hela-S3	cervix
15	chr10:90780600-90789600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:90780600-90789600	Weak transcription	Brain Hippocampus Middle	brain
17	chr10:90780600-90789600	Weak transcription	Left Ventricle	heart
18	chr10:90780600-90789800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr10:90780600-90791000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr10:90780600-90791800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr10:90780600-90791800	Weak transcription	HSMM	muscle
22	chr10:90780600-90792000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr10:90780600-90792400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr10:90780800-90791800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:90780800-90804200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr10:90781000-90789600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr10:90781000-90790800	Weak transcription	Lung	lung
28	chr10:90781000-90791600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr10:90781000-90791800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr10:90781200-90791800	Weak transcription	Fetal Thymus	thymus
31	chr10:90781400-90790600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr10:90782600-90790600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:90783000-90790600	Weak transcription	HMEC	breast
34	chr10:90783200-90791400	Weak transcription	NHEK	skin
35	chr10:90783200-90791600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:90783400-90791400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:90784400-90791600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr10:90784600-90790600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr10:90785200-90789600	Weak transcription	Liver	Liver
40	chr10:90785800-90789600	Weak transcription	HSMMtube	muscle
41	chr10:90785800-90791400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr10:90786000-90790600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr10:90786200-90789600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr10:90786400-90789600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr10:90786600-90791800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr10:90788400-90792800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr10:90788600-90789800	Enhancers	Ovary	ovary
48	chr10:90788600-90792000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr10:90788800-90789600	Enhancers	Fetal Lung	lung
50	chr10:90788800-90792800	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links