Variant report

Variant	rs3829165
Chromosome Location	chr10:1067665-1067666
allele	C/T
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	POLR2A	chr10:1066395-1067738	K562	blood:	n/a	n/a
2	POLR2A	chr10:1067479-1067715	U87	brain:	n/a	n/a
3	POLR2A	chr10:1067595-1067908	MCF-7	breast:	n/a	n/a
4	POLR2A	chr10:1066414-1067834	HepG2	liver:	n/a	n/a
5	POLR2A	chr10:1067230-1067734	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr10:1065029-1067893	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr10:1064828-1067879	K562	blood:	n/a	n/a
8	POLR2A	chr10:1066397-1067807	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:1066440-1067702	GM12891	blood:	n/a	n/a
10	POLR2A	chr10:1064790-1067937	A549	lung:	n/a	n/a
11	POLR2A	chr10:1066060-1067702	NB4	blood:	n/a	n/a
12	POLR2A	chr10:1066306-1067667	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:1065509..1068424-chr10:1086745..1089649,3	K562	blood:
2	chr10:1066057..1068191-chr10:1094760..1097466,2	MCF-7	breast:
3	chr10:1066230..1068078-chr10:1069655..1072615,2	K562	blood:

Variant related genes	Relation type
IDI2-AS1	TF binding region
ENSG00000238924	Chromatin interaction
ENSG00000067064	Chromatin interaction
ENSG00000148377	Chromatin interaction
ENSG00000047056	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12569676	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12768746	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12777134	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12782861	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2472533	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35405102	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3750729	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3793777	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56289911	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7079726	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7082272	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7923347	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS 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	43 gene(s)	inside rSNPs	diseases
4	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv1050577	chr10:986723-1277854	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv540409	chr10:986723-1277854	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949405	chr10:1010464-1376105	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv1048254	chr10:1016006-1146595	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
17	nsv1040178	chr10:1024910-1126104	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv540410	chr10:1024910-1126104	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
19	nsv894722	chr10:1058837-1274538	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
20	nsv1046220	chr10:1064024-1188998	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
21	nsv549767	chr10:1064940-1073684	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3829165	GTPBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1035000-1094000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:1038600-1068000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:1038800-1067800	Strong transcription	Skeletal Muscle Female	skeletal muscle
4	chr10:1041200-1067800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr10:1046800-1068600	Weak transcription	Right Atrium	heart
6	chr10:1049400-1071200	Strong transcription	A549	lung
7	chr10:1049600-1071600	Weak transcription	Fetal Heart	heart
8	chr10:1060000-1091600	Weak transcription	Hela-S3	cervix
9	chr10:1063200-1067800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr10:1063200-1068400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:1063200-1092000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr10:1063600-1068600	Weak transcription	Brain Substantia Nigra	brain
13	chr10:1063600-1068800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr10:1063600-1088200	Weak transcription	Fetal Brain Male	brain
15	chr10:1064000-1067800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr10:1064000-1083000	Weak transcription	NHDF-Ad	bronchial
17	chr10:1064000-1084400	Weak transcription	Colonic Mucosa	Colon
18	chr10:1064000-1088400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr10:1064200-1070000	Weak transcription	Psoas Muscle	Psoas
20	chr10:1064400-1082600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr10:1065000-1068200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr10:1065000-1068400	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr10:1065200-1084800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr10:1065400-1068400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr10:1065400-1068400	Weak transcription	Small Intestine	intestine
26	chr10:1065400-1082800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr10:1065600-1068200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr10:1065600-1068600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:1065600-1068600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr10:1065600-1083800	Weak transcription	Fetal Lung	lung
31	chr10:1065600-1086000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:1065600-1086200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr10:1065800-1068400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr10:1065800-1068600	Weak transcription	Brain Anterior Caudate	brain
35	chr10:1065800-1082600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr10:1065800-1086200	Weak transcription	Colon Smooth Muscle	Colon
37	chr10:1065800-1087800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr10:1066000-1070200	Weak transcription	K562	blood
39	chr10:1066000-1080800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr10:1066000-1081000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr10:1066000-1081200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr10:1066000-1082000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr10:1066000-1082400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr10:1066000-1082600	Weak transcription	Aorta	Aorta
45	chr10:1066000-1083000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr10:1066000-1086000	Weak transcription	HSMMtube	muscle
47	chr10:1066200-1068400	Weak transcription	Brain Angular Gyrus	brain
48	chr10:1066200-1069800	Weak transcription	Adipose Nuclei	Adipose
49	chr10:1066200-1070000	Weak transcription	Osteobl	bone
50	chr10:1066200-1079600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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