Variant report

Variant	rs4262801
Chromosome Location	chr12:12058411-12058412
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12056694..12059278-chr12:12764602..12766509,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111269	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10743969	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10845419	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11054500	0.92[EUR][1000 genomes]
rs3863339	0.91[EUR][1000 genomes]
rs3983843	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7486997	0.83[ASN][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	nsv832331	chr12:11925095-12114451	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv898804	chr12:12058411-12202173	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4262801	CD69	cis	cerebellum	SCAN
rs4262801	CLEC2A	cis	parietal	SCAN
rs4262801	PLBD1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12036000-12059200	Weak transcription	NHLF	lung
2	chr12:12046400-12059000	Weak transcription	Osteobl	bone
3	chr12:12047600-12058800	Weak transcription	HSMM	muscle
4	chr12:12047600-12059000	Weak transcription	NH-A	brain
5	chr12:12048200-12059400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:12049000-12058600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:12049000-12059800	Enhancers	Fetal Thymus	thymus
8	chr12:12055200-12058600	Weak transcription	Primary T cells from cord blood	blood
9	chr12:12055400-12059000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:12055400-12059200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:12055600-12058600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:12055800-12059000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:12056200-12059000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr12:12056200-12059000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:12056400-12058600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:12056400-12058600	Weak transcription	GM12878-XiMat	blood
17	chr12:12056400-12058800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:12056600-12058600	Weak transcription	Thymus	Thymus
19	chr12:12056600-12058800	Weak transcription	Dnd41	blood
20	chr12:12056800-12059000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:12057800-12059000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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