Variant report

Variant	rs2540229
Chromosome Location	chr2:39944055-39944056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39922964..39925781-chr2:39942136..39944750,2	MCF-7	breast:
2	chr2:39938168..39939735-chr2:39943437..39945317,2	K562	blood:
3	chr2:39941387..39944301-chr2:39949793..39952707,2	MCF-7	breast:
4	chr2:39933275..39938077-chr2:39941902..39946482,5	K562	blood:

Variant related genes	Relation type
ENSG00000152154	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10207589	0.87[GIH][hapmap];0.81[JPT][hapmap]
rs1861243	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1978327	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2058620	0.80[EUR][1000 genomes]
rs2110656	0.83[MEX][hapmap]
rs2160198	0.84[CEU][hapmap]
rs2160199	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2192686	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2215958	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2241115	0.88[JPT][hapmap]
rs2373688	0.84[EUR][1000 genomes]
rs2540226	0.83[EUR][1000 genomes]
rs2540227	0.82[EUR][1000 genomes]
rs2540228	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2540235	0.86[EUR][1000 genomes]
rs2716681	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2716699	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2716704	0.82[EUR][1000 genomes]
rs2716730	0.80[EUR][1000 genomes]
rs6722610	0.87[GIH][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap]
rs7565954	0.83[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs7590912	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs7591296	0.81[EUR][1000 genomes]
rs7591347	0.81[EUR][1000 genomes]
rs8265	0.82[AMR][1000 genomes]
rs917962	0.81[GIH][hapmap];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	nsv873889	chr2:39830183-39950482	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2540229	THUMPD2	cis	parietal	SCAN
rs2540229	THUMPD2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39925000-39957600	Weak transcription	Fetal Stomach	stomach
2	chr2:39925200-39950000	Weak transcription	Left Ventricle	heart
3	chr2:39931400-39957600	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:39931600-39945800	Weak transcription	Aorta	Aorta
5	chr2:39936600-39950600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:39937400-39948400	Weak transcription	Fetal Heart	heart
7	chr2:39938000-39957600	Weak transcription	Fetal Brain Female	brain
8	chr2:39938200-39950600	Weak transcription	HSMMtube	muscle
9	chr2:39938400-39950000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:39938800-39947800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:39940400-39947000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:39940800-39950800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:39942000-39963000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:39942400-39947600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:39943200-39944200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:39943200-39946600	Weak transcription	Brain Anterior Caudate	brain
17	chr2:39943200-39956200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:39943400-39946200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:39943400-39946400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:39943600-39946000	Weak transcription	Brain Angular Gyrus	brain

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