Variant report

Variant	rs564117
Chromosome Location	chr19:35718938-35718939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10419261	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs12979792	0.83[CEU][hapmap];0.92[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12986033	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs13345192	0.83[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs1633922	0.84[YRI][hapmap]
rs2073899	0.83[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs2280744	0.83[CEU][hapmap]
rs2280745	0.91[CEU][hapmap]
rs482324	0.81[YRI][hapmap]
rs502926	0.89[YRI][hapmap]
rs541169	0.81[YRI][hapmap]
rs542977	0.81[YRI][hapmap]
rs565704	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs569480	0.82[AFR][1000 genomes]
rs62112772	0.81[EUR][1000 genomes]
rs7256866	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv1066553	chr19:35698638-35749563	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	esv2763203	chr19:35700047-35738400	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs564117	SLC22A15	trans	cerebellum	SCAN
rs564117	SERTAD3	cis	cerebellum	SCAN
rs564117	ZFP36	cis	parietal	SCAN
rs564117	HNRNPUL1	cis	cerebellum	SCAN
rs564117	U2AF1L4	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35716400-35724400	Weak transcription	Lung	lung
2	chr19:35717000-35719000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr19:35717000-35722800	Weak transcription	Spleen	Spleen
4	chr19:35717600-35720200	Enhancers	Brain Hippocampus Middle	brain
5	chr19:35717800-35720000	Enhancers	Brain Substantia Nigra	brain
6	chr19:35718200-35719200	Weak transcription	Brain Angular Gyrus	brain
7	chr19:35718400-35719000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr19:35718600-35720000	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr19:35718800-35719200	Enhancers	K562	blood
10	chr19:35718800-35719600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:35718800-35719600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:35718800-35720200	Enhancers	Brain Cingulate Gyrus	brain

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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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