Variant report

Variant	rs2160199
Chromosome Location	chr2:39930191-39930192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39924048..39926924-chr2:39929388..39930990,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152154	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10170462	0.84[CEU][hapmap]
rs10186346	0.84[CEU][hapmap]
rs10207589	0.82[CHB][hapmap];0.93[GIH][hapmap]
rs11124693	0.82[CHB][hapmap]
rs13401182	0.86[EUR][1000 genomes]
rs1861243	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1861244	0.84[CEU][hapmap]
rs1978327	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2110656	0.83[MEX][hapmap]
rs2160198	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2192685	0.82[CHD][hapmap]
rs2192686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215958	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241115	0.82[CHB][hapmap]
rs2540228	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2540229	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]
rs2540235	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2540247	0.84[CEU][hapmap]
rs2540255	0.83[CEU][hapmap]
rs2716681	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2716694	0.84[CEU][hapmap]
rs2716699	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2716704	0.82[EUR][1000 genomes]
rs3815510	0.82[CHB][hapmap]
rs4365444	0.83[EUR][1000 genomes]
rs4644998	0.83[EUR][1000 genomes]
rs6722610	0.82[CHB][hapmap];0.93[GIH][hapmap];0.80[TSI][hapmap]
rs7565954	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs7590912	0.82[CHD][hapmap];0.93[GIH][hapmap]
rs8265	0.85[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs917961	0.86[CHD][hapmap];1.00[YRI][hapmap]
rs917964	0.84[CEU][hapmap]
rs949812	0.84[CEU][hapmap]
rs949813	0.84[CEU][hapmap]

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
rs2160199	THUMPD2	cis	parietal	SCAN
rs2160199	THUMPD2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39923600-39935200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39925000-39957600	Weak transcription	Fetal Stomach	stomach
3	chr2:39925200-39950000	Weak transcription	Left Ventricle	heart
4	chr2:39929800-39930200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:39929800-39932600	Weak transcription	HSMMtube	muscle
6	chr2:39929800-39932800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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