Variant report

Variant	rs1892252
Chromosome Location	chr6:25772639-25772640
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1165194	1.00[JPT][hapmap]
rs1165198	1.00[JPT][hapmap]
rs16890967	1.00[JPT][hapmap]
rs17341475	1.00[JPT][hapmap]
rs2154221	1.00[JPT][hapmap]
rs2762352	0.82[JPT][hapmap]
rs3734525	1.00[JPT][hapmap]
rs3734526	1.00[JPT][hapmap]
rs3823151	0.83[GIH][hapmap]
rs4481423	1.00[JPT][hapmap]
rs4712972	0.91[EUR][1000 genomes]
rs501220	1.00[GIH][hapmap]
rs523383	1.00[GIH][hapmap]
rs579996	0.83[GIH][hapmap]
rs6910549	0.86[CEU][hapmap]
rs7750960	1.00[CHB][hapmap]
rs9348693	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv969355	chr6:25733459-25779530	Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1892252	CMAH	cis	parietal	SCAN
rs1892252	HIST1H2BM	cis	cerebellum	SCAN
rs1892252	HIST1H2BH	cis	cerebellum	SCAN
rs1892252	HIST1H4E	cis	cerebellum	SCAN
rs1892252	HIST1H2AK	cis	parietal	SCAN
rs1892252	ZNF192	cis	cerebellum	SCAN
rs1892252	HIST1H2AC	cis	cerebellum	SCAN
rs1892252	ACOT13	cis	parietal	SCAN
rs1892252	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs1892252	OR2B2	cis	parietal	SCAN
rs1892252	HIST1H4F	cis	parietal	SCAN
rs1892252	ZSCAN23	cis	cerebellum	SCAN
rs1892252	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs1892252	BTN3A2	cis	lymphoblastoid	seeQTL
rs1892252	BTN3A2	cis	multi-tissue	Pritchard
rs1892252	ZSCAN23	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25758600-25777200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:25762200-25780400	Strong transcription	Liver	Liver
3	chr6:25765000-25773200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:25770800-25773200	Weak transcription	Pancreas	Pancrea
5	chr6:25770800-25776800	Weak transcription	Placenta	Placenta
6	chr6:25770800-25780000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:25771800-25774600	Weak transcription	Fetal Intestine Small	intestine
8	chr6:25772600-25773600	Strong transcription	Duodenum Mucosa	Duodenum
9	chr6:25772600-25774000	Strong transcription	Fetal Intestine Large	intestine
10	chr6:25772600-25775000	Strong transcription	Rectal Mucosa Donor 29	rectum

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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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