Variant report

Variant	rs59069340
Chromosome Location	chr5:40699365-40699366
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10056345	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10060234	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10064175	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1097546	0.85[ASN][1000 genomes]
rs13354346	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13355305	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154268	0.85[ASN][1000 genomes]
rs154275	0.85[ASN][1000 genomes]
rs154280	0.85[ASN][1000 genomes]
rs154284	0.85[ASN][1000 genomes]
rs1644962	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs171605	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs193864	0.83[ASN][1000 genomes]
rs2161521	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249413	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249414	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs249416	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs249420	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs249422	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249423	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249425	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs249428	0.85[ASN][1000 genomes]
rs249429	0.85[ASN][1000 genomes]
rs257009	0.84[ASN][1000 genomes]
rs28569300	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29740	0.85[ASN][1000 genomes]
rs29742	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29743	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs29744	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs369940	0.85[EUR][1000 genomes]
rs4277957	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285273	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315964	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315965	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432071	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs434778	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4383756	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447810	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs453037	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4573034	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs461404	0.85[ASN][1000 genomes]
rs466108	0.85[ASN][1000 genomes]
rs466962	0.83[ASN][1000 genomes]
rs4957344	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59920139	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451535	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451537	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871999	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6896993	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708680	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726237	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7733162	0.80[AMR][1000 genomes]
rs7737044	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs837101	0.84[ASN][1000 genomes]

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	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	esv3432300	chr5:40698244-40726882	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59069340	RPL37	Cis_1M	lymphoblastoid	RTeQTL
rs59069340	TTC33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40684000-40700600	Weak transcription	Left Ventricle	heart
2	chr5:40684600-40700400	Weak transcription	Right Ventricle	heart
3	chr5:40688400-40700400	Weak transcription	Stomach Mucosa	stomach
4	chr5:40688800-40718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:40692200-40701800	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:40692400-40741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:40692800-40700400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:40692800-40700400	Weak transcription	Esophagus	oesophagus
9	chr5:40692800-40700400	Weak transcription	Gastric	stomach
10	chr5:40692800-40700400	Weak transcription	Pancreas	Pancrea
11	chr5:40692800-40700400	Weak transcription	Small Intestine	intestine
12	chr5:40692800-40700600	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr5:40692800-40702400	Weak transcription	Colonic Mucosa	Colon
14	chr5:40692800-40721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:40692800-40733800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:40692800-40735000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:40693000-40700800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr5:40693000-40701800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:40693000-40701800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:40693000-40702000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:40693000-40702000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr5:40693600-40727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:40693800-40700000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:40694600-40700400	Weak transcription	Lung	lung
25	chr5:40694600-40700600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:40694800-40700200	Weak transcription	Fetal Intestine Large	intestine
27	chr5:40694800-40700400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:40694800-40700400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:40694800-40700400	Weak transcription	Aorta	Aorta
30	chr5:40694800-40700400	Weak transcription	Fetal Stomach	stomach
31	chr5:40694800-40700400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:40694800-40700400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:40694800-40700400	Weak transcription	Spleen	Spleen
34	chr5:40694800-40700600	Weak transcription	HUVEC	blood vessel
35	chr5:40694800-40701600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:40694800-40701600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:40694800-40702200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:40694800-40721000	Weak transcription	Thymus	Thymus
39	chr5:40695000-40700400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:40695000-40700400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:40695000-40701800	Weak transcription	Primary B cells from peripheral blood	blood
42	chr5:40695200-40699600	Weak transcription	Dnd41	blood
43	chr5:40695200-40700200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr5:40695200-40700600	Weak transcription	Adipose Nuclei	Adipose
45	chr5:40695200-40701800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr5:40695200-40715800	Weak transcription	Primary B cells from cord blood	blood
47	chr5:40695200-40727000	Weak transcription	HSMM	muscle
48	chr5:40695400-40700400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr5:40695600-40700400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:40695800-40700200	Weak transcription	Fetal Intestine Small	intestine

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