Variant report

Variant	rs12596240
Chromosome Location	chr16:52103123-52103124
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11076316	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11076320	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12444436	0.99[EUR][1000 genomes]
rs12599241	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1582316	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1582318	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1582321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1582322	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1582323	0.99[EUR][1000 genomes]
rs1582325	0.99[EUR][1000 genomes]
rs1582326	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs1582327	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1592481	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1592483	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1592484	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1592487	0.80[ASN][1000 genomes]
rs1592488	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1600002	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1600003	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1861323	0.85[ASN][1000 genomes]
rs1861324	0.98[ASN][1000 genomes]
rs1861325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861326	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1861328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2059233	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2194289	0.80[AMR][1000 genomes]
rs2194291	0.86[ASN][1000 genomes]
rs2216741	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs256591	0.80[ASN][1000 genomes]
rs33362	0.80[ASN][1000 genomes]
rs3743794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42771	0.85[ASN][1000 genomes]
rs9635511	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9652633	0.80[ASN][1000 genomes]

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	nsv492248	chr16:51681902-52456082	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv34024	chr16:51878565-52316530	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv827650	chr16:52067728-52124369	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1058257	chr16:52093549-52271815	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:52101400-52110400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr16:52101600-52104200	Enhancers	Brain Hippocampus Middle	brain
3	chr16:52101600-52107600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr16:52102000-52103600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr16:52102200-52103600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr16:52102600-52104400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr16:52102600-52104400	Enhancers	Brain Germinal Matrix	brain
8	chr16:52102800-52103400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr16:52102800-52103800	Weak transcription	Small Intestine	intestine
10	chr16:52102800-52104200	Enhancers	Brain Angular Gyrus	brain
11	chr16:52102800-52104200	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr16:52102800-52105000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr16:52103000-52103800	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr16:52103000-52104000	Weak transcription	Brain Anterior Caudate	brain
15	chr16:52103000-52104000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr16:52103000-52104000	Weak transcription	Fetal Stomach	stomach
17	chr16:52103000-52104000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr16:52103000-52104000	Weak transcription	Stomach Mucosa	stomach
19	chr16:52103000-52104200	Enhancers	Brain Cingulate Gyrus	brain
20	chr16:52103000-52104200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr16:52103000-52104200	Enhancers	Brain Substantia Nigra	brain
22	chr16:52103000-52106600	Weak transcription	Fetal Lung	lung
23	chr16:52103000-52112600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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