Variant report

Variant	rs3759126
Chromosome Location	chr12:50343862-50343863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1077520	0.87[CEU][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs2878771	0.87[CEU][hapmap]
rs34119994	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3741559	0.81[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs402813	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs403201	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs426496	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs439779	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs467199	0.94[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61926092	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv899072	chr12:50326176-50379667	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899073	chr12:50335628-50360461	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	esv1802978	chr12:50341465-50355864	Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	esv1847541	chr12:50341465-50355864	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	esv1851851	chr12:50341610-50355864	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3759126	SLC11A2	cis	cerebellum	SCAN
rs3759126	KCNH3	cis	parietal	SCAN
rs3759126	PRPF40B	cis	cerebellum	SCAN
rs3759126	SNORA2B	cis	parietal	SCAN
rs3759126	NCKAP5L	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50338800-50344600	Weak transcription	Spleen	Spleen
2	chr12:50339400-50353600	Weak transcription	Right Atrium	heart
3	chr12:50339600-50344200	Weak transcription	Pancreas	Pancrea
4	chr12:50340200-50346000	Weak transcription	Lung	lung
5	chr12:50340800-50344000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:50342200-50345400	Weak transcription	Hela-S3	cervix
7	chr12:50342400-50346000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:50343200-50345800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr12:50343600-50344000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:50343600-50344000	Enhancers	Fetal Kidney	kidney
11	chr12:50343800-50344000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr12:50343800-50344400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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

what's new

Quick links