Variant report

Variant	rs2405304
Chromosome Location	chr1:224391373-224391374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224368986..224373517-chr1:224390991..224394171,5	MCF-7	breast:
2	chr1:224385148..224386863-chr1:224389566..224391471,2	MCF-7	breast:
3	chr1:224386204..224388936-chr1:224390782..224393478,2	K562	blood:
4	chr1:224369479..224372718-chr1:224391156..224393202,3	K562	blood:
5	chr1:224391205..224393756-chr1:224397640..224399675,2	MCF-7	breast:
6	chr1:224387475..224389159-chr1:224391292..224393986,3	MCF-7	breast:
7	chr1:224308298..224310827-chr1:224391255..224393377,2	K562	blood:
8	chr1:224390656..224393223-chr1:224397732..224400905,3	K562	blood:
9	chr1:224379393..224381215-chr1:224390955..224393182,2	K562	blood:
10	chr1:224391151..224394255-chr1:224397647..224399379,3	MCF-7	breast:
11	chr1:224391181..224392775-chr1:224402864..224405337,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000232628	Chromatin interaction
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10916470	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916514	0.82[EUR][1000 genomes]
rs11810089	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1401320	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2139155	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2176600	0.88[ASN][1000 genomes]
rs36086207	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653996	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61826414	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6666295	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669401	0.88[ASN][1000 genomes]
rs6678942	0.88[ASN][1000 genomes]
rs6689187	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7543863	0.82[EUR][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	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
3	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2405304	RP11-365O16.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2405304	FBXO28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224372600-224392400	Weak transcription	Ovary	ovary
2	chr1:224372600-224392600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:224372800-224392000	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:224373200-224392400	Weak transcription	Colonic Mucosa	Colon
5	chr1:224373400-224392400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:224373400-224392400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:224373400-224392600	Weak transcription	Psoas Muscle	Psoas
8	chr1:224373600-224392400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:224373800-224392400	Weak transcription	Esophagus	oesophagus
10	chr1:224373800-224392400	Weak transcription	Fetal Heart	heart
11	chr1:224373800-224392400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:224374000-224392400	Weak transcription	Pancreas	Pancrea
13	chr1:224377400-224392400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:224377800-224392400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:224380400-224392400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:224381400-224391400	Weak transcription	K562	blood
17	chr1:224381400-224392000	Weak transcription	HUVEC	blood vessel
18	chr1:224381400-224392400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:224381400-224392400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:224381600-224392400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:224381600-224392400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:224381600-224392600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:224381600-224393400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:224381800-224392400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:224382000-224392400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:224382000-224392400	Weak transcription	Thymus	Thymus
27	chr1:224382200-224392000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:224382200-224392200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:224382400-224392400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:224382400-224392400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:224382400-224392400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:224382400-224392400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:224382600-224392000	Weak transcription	Lung	lung
34	chr1:224383200-224392400	Weak transcription	Primary T cells from cord blood	blood
35	chr1:224383600-224391400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:224383800-224392600	Weak transcription	Aorta	Aorta
37	chr1:224384000-224393200	Weak transcription	Small Intestine	intestine
38	chr1:224385200-224392400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:224385400-224392000	Weak transcription	Fetal Brain Male	brain
40	chr1:224388800-224392200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:224389400-224392400	Weak transcription	Gastric	stomach
42	chr1:224389600-224391400	Weak transcription	Brain Anterior Caudate	brain
43	chr1:224389600-224391600	Weak transcription	Fetal Kidney	kidney
44	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
45	chr1:224390200-224392200	Weak transcription	Fetal Intestine Small	intestine
46	chr1:224390400-224392400	Enhancers	Primary B cells from cord blood	blood
47	chr1:224390400-224392400	Enhancers	Primary B cells from peripheral blood	blood
48	chr1:224390600-224391400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:224390600-224391400	Enhancers	Fetal Muscle Leg	muscle
50	chr1:224390600-224391800	Enhancers	Fetal Thymus	thymus

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