Variant report

Variant	rs10186346
Chromosome Location	chr2:39914192-39914193
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	chr2:39605627..39608331-chr2:39913842..39916545,2	MCF-7	breast:
2	chr2:39892126..39893680-chr2:39911283..39914274,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000152154	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10170462	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12712652	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12989245	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13384364	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13405084	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13409487	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17024145	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs1861244	1.00[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2041736	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2058618	0.96[CEU][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs2160199	0.84[CEU][hapmap]
rs2540200	0.87[EUR][1000 genomes]
rs2540247	1.00[CEU][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2540248	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2540249	0.92[EUR][1000 genomes]
rs2540250	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2540251	0.92[EUR][1000 genomes]
rs2540252	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2540255	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2716682	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2716683	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2716684	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2716686	0.91[EUR][1000 genomes]
rs2716687	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2716688	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2716690	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2716691	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2716692	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2716693	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2716694	1.00[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2716732	0.88[EUR][1000 genomes]
rs2716737	0.88[EUR][1000 genomes]
rs2716738	0.87[EUR][1000 genomes]
rs4670952	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4670954	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6707177	0.96[EUR][1000 genomes]
rs6711206	0.93[EUR][1000 genomes]
rs917964	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs949812	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs949813	1.00[CEU][hapmap];0.87[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10186346	THUMPD2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39905400-39916600	Enhancers	Fetal Heart	heart
2	chr2:39907600-39922200	Weak transcription	HSMM	muscle
3	chr2:39911800-39915000	Enhancers	Right Atrium	heart
4	chr2:39911800-39915800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:39911800-39916200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:39912400-39914400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:39913000-39914200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:39913000-39914800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:39913200-39914200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr2:39913200-39914200	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr2:39913200-39914400	Enhancers	Fetal Brain Male	brain
12	chr2:39913200-39915600	Weak transcription	Left Ventricle	heart
13	chr2:39913400-39914400	Weak transcription	Lung	lung
14	chr2:39913400-39915400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:39913400-39917200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:39913600-39914800	Weak transcription	Brain Germinal Matrix	brain
17	chr2:39913600-39914800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr2:39913800-39914200	Enhancers	Fetal Lung	lung
19	chr2:39913800-39914800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:39913800-39916600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:39914000-39914200	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr2:39914000-39915600	Weak transcription	Fetal Brain Female	brain
23	chr2:39914000-39916400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:39914000-39918800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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