Variant report

Variant	rs56190511
Chromosome Location	chr10:1068067-1068068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000047056	Chromatin interaction
ENSG00000238924	Chromatin interaction
ENSG00000148377	Chromatin interaction
ENSG00000067064	Chromatin interaction

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

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

rs_ID	r²[population]
rs12241632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12269003	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13377037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17155821	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3793780	0.91[ASN][1000 genomes]
rs3793781	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56183119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58134754	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7075830	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7098169	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7099063	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74117668	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[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
rs56190511	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 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	chr10:1046800-1068600	Weak transcription	Right Atrium	heart
3	chr10:1049400-1071200	Strong transcription	A549	lung
4	chr10:1049600-1071600	Weak transcription	Fetal Heart	heart
5	chr10:1060000-1091600	Weak transcription	Hela-S3	cervix
6	chr10:1063200-1068400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr10:1063200-1092000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr10:1063600-1068600	Weak transcription	Brain Substantia Nigra	brain
9	chr10:1063600-1068800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr10:1063600-1088200	Weak transcription	Fetal Brain Male	brain
11	chr10:1064000-1083000	Weak transcription	NHDF-Ad	bronchial
12	chr10:1064000-1084400	Weak transcription	Colonic Mucosa	Colon
13	chr10:1064000-1088400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr10:1064200-1070000	Weak transcription	Psoas Muscle	Psoas
15	chr10:1064400-1082600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr10:1065000-1068200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:1065000-1068400	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr10:1065200-1084800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr10:1065400-1068400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr10:1065400-1068400	Weak transcription	Small Intestine	intestine
21	chr10:1065400-1082800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr10:1065600-1068200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr10:1065600-1068600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr10:1065600-1068600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:1065600-1083800	Weak transcription	Fetal Lung	lung
26	chr10:1065600-1086000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr10:1065600-1086200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr10:1065800-1068400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr10:1065800-1068600	Weak transcription	Brain Anterior Caudate	brain
30	chr10:1065800-1082600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr10:1065800-1086200	Weak transcription	Colon Smooth Muscle	Colon
32	chr10:1065800-1087800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr10:1066000-1070200	Weak transcription	K562	blood
34	chr10:1066000-1080800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr10:1066000-1081000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:1066000-1081200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr10:1066000-1082000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr10:1066000-1082400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr10:1066000-1082600	Weak transcription	Aorta	Aorta
40	chr10:1066000-1083000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr10:1066000-1086000	Weak transcription	HSMMtube	muscle
42	chr10:1066200-1068400	Weak transcription	Brain Angular Gyrus	brain
43	chr10:1066200-1069800	Weak transcription	Adipose Nuclei	Adipose
44	chr10:1066200-1070000	Weak transcription	Osteobl	bone
45	chr10:1066200-1079600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:1066200-1082200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr10:1066200-1082200	Weak transcription	NH-A	brain
48	chr10:1066200-1082400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr10:1066200-1083200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr10:1066200-1083400	Weak transcription	Liver	Liver

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