Variant report

Variant	rs11754080
Chromosome Location	chr6:24284244-24284245
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24283175..24284815-chr6:24359561..24361041,12	MCF-7	breast:
2	chr6:24282520..24284715-chr6:24405070..24407671,2	MCF-7	breast:
3	chr6:24281828..24284999-chr6:24354828..24358110,4	MCF-7	breast:
4	chr2:27975663..27977843-chr6:24284070..24286827,2	MCF-7	breast:
5	chr6:24282573..24285599-chr6:24386965..24389138,3	K562	blood:
6	chr6:24281863..24285014-chr6:24356615..24360077,4	MCF-7	breast:
7	chr6:24281775..24284260-chr6:24359000..24360636,2	MCF-7	breast:
8	chr6:24282327..24284460-chr6:24388227..24391209,2	MCF-7	breast:
9	chr6:24282475..24284958-chr6:24289359..24291059,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000146038	Chromatin interaction
ENSG00000146049	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1091045	0.93[ASN][1000 genomes]
rs1091046	0.95[ASN][1000 genomes]
rs1091047	0.96[ASN][1000 genomes]
rs10946689	0.81[JPT][hapmap]
rs1109332	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11754278	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11757997	0.87[ASN][1000 genomes]
rs11757999	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17302512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17302582	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17302729	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2262443	0.94[ASN][1000 genomes]
rs2296537	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296538	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328208	0.94[ASN][1000 genomes]
rs28921369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28924368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789224	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789225	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3789227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804327	0.96[ASN][1000 genomes]
rs58592947	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59166901	0.83[ASN][1000 genomes]
rs59975176	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60387283	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60537291	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62400411	0.93[ASN][1000 genomes]
rs62400414	0.95[ASN][1000 genomes]
rs62400417	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62403468	0.81[ASN][1000 genomes]
rs66492054	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66531067	0.96[AFR][1000 genomes]
rs66735044	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67482549	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67939976	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68182041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72828999	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72830803	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72830805	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72830807	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72830822	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72830828	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72830832	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72830841	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72830842	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72830843	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72830851	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72830854	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72830855	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72830859	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72830865	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72830874	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73394078	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73394097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394100	0.94[AFR][1000 genomes]
rs73396004	0.94[AFR][1000 genomes]
rs73396022	0.92[AFR][1000 genomes]
rs73396024	0.88[AFR][1000 genomes]
rs807712	0.97[EUR][1000 genomes];0.97[ASN][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	nsv1029930	chr6:23481989-24289948	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427746	chr6:24221299-24305709	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24282600-24284600	Enhancers	Fetal Muscle Leg	muscle
2	chr6:24282800-24284600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:24282800-24284600	Enhancers	GM12878-XiMat	blood
4	chr6:24283000-24284400	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:24283000-24284400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:24283000-24284400	Enhancers	Liver	Liver
7	chr6:24283000-24284400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr6:24283000-24284400	Enhancers	Fetal Stomach	stomach
9	chr6:24283000-24284600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:24283400-24284400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:24283400-24284400	Enhancers	Fetal Lung	lung
12	chr6:24283400-24284600	Enhancers	Colon Smooth Muscle	Colon
13	chr6:24283400-24284600	Enhancers	Fetal Muscle Trunk	muscle
14	chr6:24283600-24284400	Enhancers	NH-A	brain
15	chr6:24283600-24284600	Enhancers	Left Ventricle	heart
16	chr6:24283800-24284400	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:24283800-24284400	Enhancers	Placenta	Placenta
18	chr6:24283800-24284400	Enhancers	Gastric	stomach
19	chr6:24283800-24285000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:24284000-24284400	Enhancers	Adipose Nuclei	Adipose
21	chr6:24284000-24284400	Enhancers	Fetal Kidney	kidney
22	chr6:24284000-24284400	Weak transcription	Pancreas	Pancrea
23	chr6:24284000-24284400	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr6:24284000-24284600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:24284000-24284600	Enhancers	A549	lung
26	chr6:24284000-24287000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:24284000-24288400	Weak transcription	Spleen	Spleen
28	chr6:24284200-24284400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:24284200-24284400	Enhancers	Hela-S3	cervix
30	chr6:24284200-24284400	Flanking Active TSS	HepG2	liver
31	chr6:24284200-24284600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:24284200-24284600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:24284200-24284600	Enhancers	Fetal Heart	heart
34	chr6:24284200-24292000	Weak transcription	Fetal Intestine Large	intestine
35	chr6:24284200-24294200	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links