Variant report

Variant	rs3131856
Chromosome Location	chr6:29607101-29607102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1233385	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1233393	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131894	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs404240	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs408623	1.00[AFR][1000 genomes];0.81[EUR][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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv969292	chr6:29604881-29612154	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3131856	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3131856	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3131856	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3131856	HLA-C	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29601800-29608600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr6:29602400-29607200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:29602600-29609200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:29602600-29609200	Weak transcription	HMEC	breast
5	chr6:29602800-29607200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:29602800-29609200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:29603000-29607200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:29603000-29608400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr6:29604200-29609200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:29606800-29607800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr6:29607000-29607400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:29607000-29607400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr6:29607000-29607600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr6:29607000-29607600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr6:29607000-29608400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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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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