Variant report

Variant	rs1541269
Chromosome Location	chr6:30103360-30103361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
TRIM40	TF binding region
ENSG00000252228	TF binding region
ENSG00000066379	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000252228	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1034326	0.91[EUR][1000 genomes]
rs1034327	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2239529	0.81[EUR][1000 genomes]
rs2427749	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2517595	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2517596	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2517597	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2517668	0.87[ASN][1000 genomes]
rs2523976	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2523977	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2523979	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2523981	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2523982	0.87[EUR][1000 genomes]
rs2523983	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2523986	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2523987	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2523988	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2844790	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2844791	0.86[EUR][1000 genomes]
rs2844792	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1541269	ZFP57	cis	multi-tissue	Pritchard
rs1541269	HLA-A	cis	multi-tissue	Pritchard
rs1541269	HLA-H	cis	multi-tissue	Pritchard
rs1541269	ZNF323	cis	parietal	SCAN
rs1541269	HLA-DQA1	cis	multi-tissue	Pritchard
rs1541269	BTN2A1	cis	parietal	SCAN
rs1541269	ZNF192	cis	cerebellum	SCAN
rs1541269	ZKSCAN3	cis	parietal	SCAN
rs1541269	HLA-C	cis	multi-tissue	Pritchard
rs1541269	ZNF192	cis	parietal	SCAN
rs1541269	BTN3A2	cis	multi-tissue	Pritchard
rs1541269	HLA-A	cis	lymphoblastoid	GTEx
rs1541269	HIST1H2BM	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30099000-30103600	Weak transcription	A549	lung
2	chr6:30099400-30103400	Weak transcription	Hela-S3	cervix
3	chr6:30101400-30104000	Enhancers	Fetal Intestine Small	intestine
4	chr6:30101800-30105000	Enhancers	Fetal Intestine Large	intestine
5	chr6:30102800-30103400	Enhancers	HepG2	liver
6	chr6:30103200-30103600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr6:30103200-30103800	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr6:30103200-30103800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr6:30103200-30103800	Enhancers	Stomach Mucosa	stomach

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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