Variant report

Variant	rs12518792
Chromosome Location	chr5:60386653-60386654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60385727..60388209-chr5:60393407..60396007,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10805374	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10939879	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10939881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10939882	0.89[AFR][1000 genomes]
rs11739952	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11951076	0.85[AFR][1000 genomes]
rs12516995	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12517310	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12518404	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12652830	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12652878	0.80[EUR][1000 genomes]
rs12653132	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12655209	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1382917	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1460961	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1471488	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1479645	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1526896	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs159535	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs159536	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs159537	0.83[AFR][1000 genomes]
rs17332824	0.80[EUR][1000 genomes]
rs17392014	0.80[EUR][1000 genomes]
rs17419290	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17444495	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1983484	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2049579	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28436304	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2898309	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34608	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34609	0.81[AFR][1000 genomes]
rs34617	0.82[AFR][1000 genomes]
rs34619	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34625	0.80[AFR][1000 genomes]
rs4642318	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647052	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4647137	0.81[EUR][1000 genomes]
rs4647150	0.80[EUR][1000 genomes]
rs4699969	0.89[AFR][1000 genomes]
rs4700402	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4700404	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700407	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55738840	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55814394	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56025209	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56031340	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56159106	0.81[AFR][1000 genomes]
rs56284222	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56350217	0.83[EUR][1000 genomes]
rs58646987	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61017995	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62365455	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62365458	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62367862	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62367872	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62367878	0.86[EUR][1000 genomes]
rs62367879	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62367885	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62367903	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6449512	0.87[EUR][1000 genomes]
rs67490467	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68104763	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs726824	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72757187	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72759206	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72759215	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7701398	0.80[EUR][1000 genomes]
rs7706753	0.87[AFR][1000 genomes]
rs7709522	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7713481	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714396	0.86[EUR][1000 genomes]
rs7722373	0.84[ASN][1000 genomes]
rs7723349	0.86[ASN][1000 genomes]
rs7723901	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7734205	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7737276	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs868791	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs888799	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1019307	chr5:60295350-60409077	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv598314	chr5:60374912-60459040	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12518792	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs12518792	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60326000-60400800	Weak transcription	Left Ventricle	heart
2	chr5:60350800-60396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:60365600-60387000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:60366400-60397400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:60367400-60386800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:60367400-60399400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr5:60367600-60398400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:60367800-60403800	Weak transcription	Primary B cells from cord blood	blood
9	chr5:60368200-60390600	Weak transcription	Fetal Intestine Small	intestine
10	chr5:60368200-60397600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr5:60368200-60402000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr5:60368400-60390200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr5:60369000-60400200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:60369400-60388200	Weak transcription	Gastric	stomach
15	chr5:60369800-60396400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:60370200-60395600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:60371600-60398000	Weak transcription	HSMM	muscle
18	chr5:60371800-60387400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:60373200-60387000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:60373200-60395600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:60378800-60395600	Weak transcription	Primary T cells from cord blood	blood
22	chr5:60378800-60403400	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:60379400-60395600	Weak transcription	Ovary	ovary
24	chr5:60379400-60403000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:60381000-60419400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:60381200-60387400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:60381400-60397600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr5:60381600-60387400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr5:60383000-60395600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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