Variant report

Variant	rs290397
Chromosome Location	chr20:52696013-52696014
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	chr20:46573682..46576531-chr20:52695158..52697078,2	MCF-7	breast:
2	chr17:56707573..56710452-chr20:52690315..52697249,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs290396	0.83[AFR][1000 genomes]
rs290398	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs379582	0.93[ASN][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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs290397	BCAS1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52693000-52701200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr20:52693400-52698600	Weak transcription	Stomach Mucosa	stomach
3	chr20:52693800-52697400	Enhancers	Primary hematopoietic stem cells	blood
4	chr20:52693800-52699200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr20:52694200-52696200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr20:52694200-52696400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr20:52694200-52697600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr20:52694400-52697400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr20:52694600-52696200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr20:52694600-52696600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr20:52694800-52696200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr20:52694800-52696200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr20:52694800-52696600	Enhancers	Primary B cells from peripheral blood	blood
14	chr20:52694800-52696600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr20:52694800-52697200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr20:52695400-52696600	Enhancers	Primary T cells from cord blood	blood
17	chr20:52695600-52696600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr20:52695600-52700200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr20:52695800-52698800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr20:52696000-52696600	Enhancers	GM12878-XiMat	blood
21	chr20:52696000-52698600	Weak transcription	A549	lung

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