Variant report

Variant	rs1060394
Chromosome Location	chr1:224380921-224380922
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224372056..224374246-chr1:224379708..224382000,2	MCF-7	breast:
2	chr1:224379393..224381215-chr1:224390955..224393182,2	K562	blood:

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10799525	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799541	0.90[CHB][hapmap]
rs11589025	0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12022755	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9661659	0.85[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	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv8857	chr1:224359943-224383023	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1060394	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1060394	FBXO28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224372400-224381000	Weak transcription	HSMMtube	muscle
2	chr1:224372400-224389200	Weak transcription	Fetal Kidney	kidney
3	chr1:224372600-224391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:224372600-224392400	Weak transcription	Ovary	ovary
5	chr1:224372600-224392600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:224372800-224381000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:224372800-224392000	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:224373000-224383600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:224373200-224382000	Weak transcription	Brain Substantia Nigra	brain
10	chr1:224373200-224392400	Weak transcription	Colonic Mucosa	Colon
11	chr1:224373400-224381200	Weak transcription	Aorta	Aorta
12	chr1:224373400-224383600	Weak transcription	Small Intestine	intestine
13	chr1:224373400-224384400	Weak transcription	Brain Germinal Matrix	brain
14	chr1:224373400-224392400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:224373400-224392400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:224373400-224392600	Weak transcription	Psoas Muscle	Psoas
17	chr1:224373600-224381000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:224373600-224381000	Weak transcription	NHDF-Ad	bronchial
19	chr1:224373600-224392400	Weak transcription	Brain Angular Gyrus	brain
20	chr1:224373800-224381000	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:224373800-224384200	Weak transcription	Fetal Brain Male	brain
22	chr1:224373800-224392400	Weak transcription	Esophagus	oesophagus
23	chr1:224373800-224392400	Weak transcription	Fetal Heart	heart
24	chr1:224373800-224392400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:224374000-224384800	Weak transcription	Stomach Mucosa	stomach
26	chr1:224374000-224391000	Weak transcription	Spleen	Spleen
27	chr1:224374000-224392400	Weak transcription	Pancreas	Pancrea
28	chr1:224374200-224382000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:224375000-224383000	Weak transcription	Gastric	stomach
30	chr1:224375200-224382200	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:224376000-224382200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:224376400-224383000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:224376800-224382000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:224377200-224382400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:224377200-224382600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:224377200-224382600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:224377200-224383200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:224377200-224383200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:224377200-224384200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:224377400-224381400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:224377400-224381600	Strong transcription	Fetal Intestine Large	intestine
42	chr1:224377400-224382000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:224377400-224382000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:224377400-224382000	Strong transcription	Adipose Nuclei	Adipose
45	chr1:224377400-224382000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:224377400-224382200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:224377400-224382200	Strong transcription	Placenta	Placenta
48	chr1:224377400-224382200	Strong transcription	Fetal Thymus	thymus
49	chr1:224377400-224382400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:224377400-224382400	Strong transcription	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links