Variant report

Variant	rs2300036
Chromosome Location	chr7:108024721-108024722
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	chr7:108022146..108024976-chr7:108095353..108098019,2	MCF-7	breast:
2	chr7:107997129..107999645-chr7:108022615..108024810,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266112	Chromatin interaction
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10245718	0.81[CEU][hapmap]
rs11971972	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11973823	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11976021	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11979596	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11983900	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12669879	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12705470	0.86[CEU][hapmap]
rs13222628	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13245242	0.81[CEU][hapmap]
rs17155637	1.00[CEU][hapmap]
rs17421351	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2108252	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2108253	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2300040	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2395995	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35429156	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6466224	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6466225	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6466226	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6954366	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6959409	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6960478	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6966107	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6969521	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7797885	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2300036	THAP5	cis	normal skin	skin_eQTL
rs2300036	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108014800-108043200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:108020000-108034200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:108021400-108040800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:108021400-108043000	Weak transcription	HMEC	breast
5	chr7:108021800-108025000	Weak transcription	A549	lung
6	chr7:108021800-108026600	Weak transcription	HUVEC	blood vessel
7	chr7:108022400-108034200	Weak transcription	Pancreas	Pancrea
8	chr7:108024000-108025400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:108024000-108033000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:108024000-108045600	Weak transcription	Brain Anterior Caudate	brain
11	chr7:108024200-108036000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:108024400-108034000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:108024400-108036000	Weak transcription	Brain Angular Gyrus	brain

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