Variant report

Variant	rs60523550
Chromosome Location	chr2:99409630-99409631
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: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	chr2:99346819..99349538-chr2:99408067..99410361,3	MCF-7	breast:
2	chr2:99393178..99396071-chr2:99408635..99411955,5	MCF-7	breast:
3	chr2:99408337..99412495-chr2:99418942..99424150,7	MCF-7	breast:
4	chr2:99386151..99388080-chr2:99407312..99410170,2	MCF-7	breast:
5	chr2:99347120..99347731-chr2:99409360..99410028,2	MCF-7	breast:
6	chr2:99408029..99409823-chr2:99425187..99427144,2	MCF-7	breast:
7	chr2:99360967..99363379-chr2:99408314..99410102,2	MCF-7	breast:
8	chr2:99345187..99349876-chr2:99408003..99411838,6	MCF-7	breast:
9	chr2:99396878..99399101-chr2:99408981..99411338,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000201070	Chromatin interaction
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs56923186	1.00[AMR][1000 genomes]
rs58738020	1.00[AMR][1000 genomes]
rs58821307	1.00[AMR][1000 genomes]
rs59365702	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60725966	1.00[AMR][1000 genomes]
rs60745907	1.00[AMR][1000 genomes]
rs61503115	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs67008211	0.81[AFR][1000 genomes]
rs72956638	1.00[AMR][1000 genomes]
rs72956659	1.00[AMR][1000 genomes]
rs72956663	1.00[AMR][1000 genomes]
rs72957625	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72957633	1.00[AMR][1000 genomes]
rs72957643	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72957654	1.00[AMR][1000 genomes]
rs72957656	1.00[AMR][1000 genomes]
rs72957660	1.00[AMR][1000 genomes]
rs72957672	1.00[AMR][1000 genomes]
rs72958630	1.00[AMR][1000 genomes]
rs72958634	1.00[AMR][1000 genomes]
rs72958636	1.00[AMR][1000 genomes]
rs72958646	1.00[AMR][1000 genomes]
rs72958649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72958653	1.00[AMR][1000 genomes]
rs72958659	1.00[AMR][1000 genomes]
rs72958661	1.00[AMR][1000 genomes]
rs72958666	1.00[AMR][1000 genomes]
rs72960709	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73965241	1.00[AMR][1000 genomes]
rs73965242	1.00[AMR][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99385800-99410400	Weak transcription	Right Atrium	heart
2	chr2:99401800-99412800	Weak transcription	Gastric	stomach
3	chr2:99403400-99412800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:99404400-99410400	Weak transcription	Brain Anterior Caudate	brain
5	chr2:99404400-99417200	Weak transcription	Stomach Mucosa	stomach
6	chr2:99404600-99411000	Weak transcription	Pancreas	Pancrea
7	chr2:99406000-99421800	Weak transcription	Spleen	Spleen
8	chr2:99406400-99409800	Weak transcription	HepG2	liver
9	chr2:99406800-99412800	Weak transcription	Thymus	Thymus
10	chr2:99407000-99412200	Weak transcription	Fetal Thymus	thymus
11	chr2:99407600-99415800	Weak transcription	Left Ventricle	heart
12	chr2:99407600-99423800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:99407800-99412000	Weak transcription	Fetal Intestine Small	intestine
14	chr2:99408000-99410600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:99408200-99412600	Weak transcription	Lung	lung
16	chr2:99408600-99410400	Weak transcription	Fetal Intestine Large	intestine
17	chr2:99408800-99409800	Enhancers	Placenta	Placenta
18	chr2:99408800-99411400	Enhancers	HMEC	breast
19	chr2:99409000-99409800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr2:99409000-99411200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:99409000-99412800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:99409000-99415600	Weak transcription	Colonic Mucosa	Colon
23	chr2:99409200-99409800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr2:99409200-99411000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:99409200-99411200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:99409200-99411400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:99409200-99425800	Weak transcription	Small Intestine	intestine
28	chr2:99409400-99410400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:99409400-99410800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:99409400-99410800	Enhancers	Fetal Brain Male	brain
31	chr2:99409400-99413800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr2:99409600-99409800	Enhancers	Fetal Lung	lung
33	chr2:99409600-99410000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:99409600-99410000	Flanking Active TSS	NHEK	skin
35	chr2:99409600-99410600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:99409600-99411200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:99409600-99426400	Weak transcription	Esophagus	oesophagus

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