Variant report

Variant	rs59920139
Chromosome Location	chr5:40700956-40700957
allele	A/G
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	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10060234	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10064175	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1097546	0.85[ASN][1000 genomes]
rs13354346	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13355305	0.90[AMR][1000 genomes];0.99[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	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249414	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs249416	0.83[AMR][1000 genomes];0.91[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	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[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	0.84[EUR][1000 genomes]
rs4277957	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285273	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315964	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4315965	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432071	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs434778	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4383756	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447810	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs453037	0.85[ASN][1000 genomes]
rs4573034	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[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	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59069340	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451535	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451537	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871999	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6896993	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708680	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726237	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7733162	0.84[AMR][1000 genomes]
rs7737044	0.90[AMR][1000 genomes];0.95[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
rs59920139	TTC33	Cis_1M	lymphoblastoid	RTeQTL
rs59920139	RPL37	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40688800-40718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:40692200-40701800	Weak transcription	Colon Smooth Muscle	Colon
3	chr5:40692400-40741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:40692800-40702400	Weak transcription	Colonic Mucosa	Colon
5	chr5:40692800-40721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:40692800-40733800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr5:40692800-40735000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:40693000-40701800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:40693000-40701800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:40693000-40702000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:40693000-40702000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:40693600-40727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:40694800-40701600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:40694800-40701600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:40694800-40702200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:40694800-40721000	Weak transcription	Thymus	Thymus
17	chr5:40695000-40701800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr5:40695200-40701800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:40695200-40715800	Weak transcription	Primary B cells from cord blood	blood
20	chr5:40695200-40727000	Weak transcription	HSMM	muscle
21	chr5:40695800-40704000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:40697000-40702200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr5:40699000-40720800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr5:40699400-40701600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:40699600-40701200	Strong transcription	Dnd41	blood
26	chr5:40700000-40701600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:40700200-40701400	Enhancers	Fetal Intestine Large	intestine
28	chr5:40700400-40701000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:40700400-40701000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:40700400-40701000	ZNF genes & repeats	Aorta	Aorta
31	chr5:40700400-40701000	ZNF genes & repeats	Esophagus	oesophagus
32	chr5:40700400-40701000	ZNF genes & repeats	Right Atrium	heart
33	chr5:40700400-40701000	Strong transcription	Right Ventricle	heart
34	chr5:40700400-40701000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
35	chr5:40700400-40701000	Enhancers	Small Intestine	intestine
36	chr5:40700400-40701000	Enhancers	Stomach Mucosa	stomach
37	chr5:40700400-40701200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
38	chr5:40700400-40701200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:40700400-40701200	Enhancers	Duodenum Mucosa	Duodenum
40	chr5:40700400-40701400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr5:40700400-40702400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
42	chr5:40700400-40702800	ZNF genes & repeats	Primary T cells from cord blood	blood
43	chr5:40700400-40706800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:40700600-40701000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:40700600-40701000	ZNF genes & repeats	Adipose Nuclei	Adipose
46	chr5:40700600-40701200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
47	chr5:40700600-40701400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
48	chr5:40700600-40703000	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr5:40700800-40701200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr5:40700800-40701200	Enhancers	Fetal Intestine Small	intestine

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