Variant report

Variant	rs10255299
Chromosome Location	chr7:111527560-111527561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:111523007..111524740-chr7:111526711..111529369,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10085411	0.85[EUR][1000 genomes]
rs10085418	0.85[EUR][1000 genomes]
rs10224457	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10230127	0.87[EUR][1000 genomes]
rs10236850	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10249065	0.91[EUR][1000 genomes]
rs10256552	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10257550	0.80[GIH][hapmap]
rs10261279	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10269918	0.89[EUR][1000 genomes]
rs10277083	0.85[EUR][1000 genomes]
rs13227802	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28657710	0.89[EUR][1000 genomes]
rs59559298	0.89[EUR][1000 genomes]
rs6466391	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6971767	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv608196	chr7:111073710-111794368	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv608215	chr7:111183610-111533520	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1021527	chr7:111194596-111851619	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv539086	chr7:111194596-111851619	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1028740	chr7:111227747-111679401	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1015267	chr7:111303294-111714771	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv539087	chr7:111303294-111714771	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv539088	chr7:111333899-111722341	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv531435	chr7:111333900-111926292	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv491934	chr7:111333900-111975504	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv532335	chr7:111411990-112054905	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
C-reactive protein and white blood cell count	22788528	GWAS catalog

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:111477000-111527600	Weak transcription	A549	lung
2	chr7:111481000-111554000	Weak transcription	Placenta	Placenta
3	chr7:111487200-111537600	Weak transcription	HepG2	liver
4	chr7:111500600-111560400	Weak transcription	Pancreas	Pancrea
5	chr7:111506000-111543200	Weak transcription	HMEC	breast
6	chr7:111514200-111540200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:111514400-111534400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr7:111514400-111556400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:111514600-111539200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:111514600-111539600	Weak transcription	Right Ventricle	heart
11	chr7:111514600-111540000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr7:111514600-111540200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:111514600-111546600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:111514800-111571000	Weak transcription	NHLF	lung
15	chr7:111515000-111534600	Weak transcription	Adipose Nuclei	Adipose
16	chr7:111515000-111537800	Weak transcription	Psoas Muscle	Psoas
17	chr7:111515000-111538000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:111515000-111554200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:111515000-111554200	Weak transcription	Esophagus	oesophagus
20	chr7:111517200-111540200	Weak transcription	Colon Smooth Muscle	Colon
21	chr7:111518200-111528000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:111519200-111558200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:111519400-111534400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:111519400-111534400	Weak transcription	Aorta	Aorta
25	chr7:111519600-111527600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:111519600-111527800	Weak transcription	Left Ventricle	heart
27	chr7:111519600-111534400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:111519600-111534400	Weak transcription	Fetal Stomach	stomach
29	chr7:111519600-111539000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr7:111519600-111540000	Weak transcription	NHEK	skin
31	chr7:111519600-111540200	Weak transcription	Brain Germinal Matrix	brain
32	chr7:111521200-111540000	Weak transcription	Fetal Brain Female	brain
33	chr7:111521400-111545400	Weak transcription	Fetal Brain Male	brain
34	chr7:111521800-111540200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr7:111521800-111578000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:111522600-111540000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:111522800-111534400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:111523800-111534600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr7:111523800-111541400	Weak transcription	Small Intestine	intestine
40	chr7:111524600-111527600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:111525000-111540000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr7:111525600-111527800	Strong transcription	Ovary	ovary
43	chr7:111525600-111533200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:111526000-111532600	Weak transcription	Brain Hippocampus Middle	brain
45	chr7:111526000-111533200	Weak transcription	Brain Anterior Caudate	brain
46	chr7:111526000-111534400	Weak transcription	Brain Substantia Nigra	brain
47	chr7:111526000-111534600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:111526200-111528600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr7:111526600-111529400	Weak transcription	Fetal Kidney	kidney
50	chr7:111526800-111555600	Weak transcription	Spleen	Spleen

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