Variant report

Variant	rs11934876
Chromosome Location	chr4:48437738-48437739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10517217	0.86[JPT][hapmap]
rs1055721	0.87[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs13105691	0.89[ASN][1000 genomes]
rs13145421	0.91[ASN][1000 genomes]
rs17655838	0.93[ASN][1000 genomes]
rs17655898	0.91[ASN][1000 genomes]
rs309890	0.80[JPT][hapmap]
rs4695382	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4695383	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6447631	0.87[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs7434434	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7441842	0.94[ASN][1000 genomes]
rs7655066	0.87[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs7662325	0.94[ASN][1000 genomes]
rs7664981	0.94[JPT][hapmap]
rs7688310	0.90[JPT][hapmap]
rs7700141	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9992736	0.90[JPT][hapmap]
rs9999482	0.90[JPT][hapmap]

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	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11934876	SLAIN2	cis	cerebellum	SCAN
rs11934876	SLAIN2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48423400-48438200	Weak transcription	Fetal Intestine Small	intestine
2	chr4:48425200-48441600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr4:48425400-48438400	Weak transcription	HSMMtube	muscle
4	chr4:48425800-48438400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:48425800-48438600	Weak transcription	Fetal Intestine Large	intestine
6	chr4:48426000-48438200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:48426000-48442000	Weak transcription	K562	blood
8	chr4:48430200-48438600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:48431000-48438400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:48433400-48438400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:48434000-48438400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:48434000-48441800	Weak transcription	Left Ventricle	heart
13	chr4:48434600-48438400	Weak transcription	Stomach Mucosa	stomach

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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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