Variant report

Variant	rs62165184
Chromosome Location	chr2:55788253-55788254
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr2:55788050-55788435	HEK293	kidney:	n/a	n/a
2	POLR2A	chr2:55788227-55788318	GM12878	blood:	n/a	n/a
3	CBX3	chr2:55787986-55788306	K562	blood:	n/a	n/a
4	ZNF143	chr2:55788198-55788258	K562	blood:	n/a	n/a
5	CBX3	chr2:55788014-55788307	K562	blood:	n/a	n/a
6	SETDB1	chr2:55788030-55788394	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000212175	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10454749	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10496050	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1058582	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1084522	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11125579	0.87[EUR][1000 genomes]
rs11125581	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17278044	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17369191	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17798852	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1823893	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975484	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1975487	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2054728	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2586947	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2586968	0.82[AMR][1000 genomes]
rs2586969	0.82[AMR][1000 genomes]
rs2586970	0.82[AMR][1000 genomes]
rs2627759	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2627776	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2627777	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2627780	0.82[AMR][1000 genomes]
rs2627782	0.83[AMR][1000 genomes]
rs35504023	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3762513	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4290693	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4312532	0.85[AFR][1000 genomes]
rs4672052	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4672054	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4672055	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4672056	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55761024	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58003472	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62165173	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62165181	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62165182	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62165183	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62165196	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62165197	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545506	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6739513	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7582278	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7594279	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7598650	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782586	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs782587	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782588	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs782590	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782594	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs782595	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs782599	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782600	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782601	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782602	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782613	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs782649	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs782650	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs782652	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs935177	0.82[AMR][1000 genomes]

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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised 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	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats 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	11 gene(s)	inside rSNPs	diseases
5	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62165184	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55748000-55793800	Weak transcription	Psoas Muscle	Psoas
2	chr2:55752600-55831400	Weak transcription	Stomach Mucosa	stomach
3	chr2:55769600-55816000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:55770400-55818200	Weak transcription	Small Intestine	intestine
5	chr2:55770600-55821600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:55770800-55815800	Strong transcription	Liver	Liver
7	chr2:55775200-55798000	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr2:55776000-55789600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:55776600-55788400	Strong transcription	Primary B cells from cord blood	blood
10	chr2:55779400-55792200	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr2:55779400-55793000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:55779400-55795000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:55779400-55798200	Strong transcription	Placenta	Placenta
14	chr2:55779400-55801400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:55779600-55793400	Strong transcription	Adipose Nuclei	Adipose
16	chr2:55779600-55797400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:55779600-55816200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:55779600-55831400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:55780000-55791600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:55780000-55792200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:55780000-55792600	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:55780000-55801400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr2:55780200-55792200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:55781000-55792000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:55781200-55792000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:55781200-55794200	Strong transcription	Fetal Lung	lung
27	chr2:55781400-55791200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:55781600-55788800	Weak transcription	Fetal Kidney	kidney
29	chr2:55781600-55808800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:55782200-55797400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:55783000-55789800	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:55783000-55791800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr2:55783200-55788600	Strong transcription	Primary T cells from cord blood	blood
34	chr2:55783400-55788400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:55783400-55792000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr2:55783600-55791000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:55783800-55789800	Strong transcription	Spleen	Spleen
38	chr2:55783800-55790200	Strong transcription	Brain Hippocampus Middle	brain
39	chr2:55783800-55790800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:55783800-55797000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:55784000-55788400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:55784000-55789600	Weak transcription	Fetal Heart	heart
43	chr2:55784000-55790600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:55784000-55790800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:55784000-55792400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:55784200-55791000	Strong transcription	Left Ventricle	heart
47	chr2:55784200-55792200	Strong transcription	Fetal Intestine Large	intestine
48	chr2:55784200-55795400	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr2:55785000-55805000	Weak transcription	NHEK	skin
50	chr2:55785400-55789000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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