Variant report

Variant	rs12770910
Chromosome Location	chr10:1050318-1050319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:1050076-1050766	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr10:1050016-1050732	HepG2	liver:	n/a	n/a
3	POLR2A	chr10:1050079-1050410	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr10:1049750-1050863	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr10:1050292-1050465	MCF-7	breast:	n/a	n/a
6	POLR2A	chr10:1049861-1050468	K562	blood:	n/a	n/a
7	POLR2A	chr10:1049723-1050392	K562	blood:	n/a	n/a
8	POLR2A	chr10:1049638-1051166	GM12892	blood:	n/a	n/a
9	POLR2A	chr10:1049819-1051029	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr10:1049478-1051100	A549	lung:	n/a	n/a
11	POLR2A	chr10:1050119-1051257	GM12892	blood:	n/a	n/a
12	POLR2A	chr10:1050261-1050792	GM12878	blood:	n/a	n/a
13	POLR2A	chr10:1050143-1051031	K562	blood:	n/a	n/a
14	ZNF263	chr10:1050119-1050992	HEK293-T-REx	kidney:	n/a	n/a
15	POLR2A	chr10:1049507-1050999	K562	blood:	n/a	n/a
16	POLR2A	chr10:1050109-1050608	HepG2	liver:	n/a	n/a
17	POLR2A	chr10:1050125-1051160	GM12892	blood:	n/a	n/a
18	POLR2A	chr10:1049804-1050994	K562	blood:	n/a	n/a
19	POLR2A	chr10:1049644-1051085	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:1048891..1050643-chr10:1061683..1063902,2	K562	blood:
2	chr10:1015085..1016586-chr10:1048514..1051399,2	MCF-7	breast:
3	chr10:1048578..1051233-chr10:1058068..1059841,2	MCF-7	breast:
4	chr10:1049525..1051510-chr10:1093462..1095993,3	MCF-7	breast:
5	chr10:1039855..1042712-chr10:1046941..1050374,3	MCF-7	breast:
6	chr10:1049830..1051331-chr10:1051501..1053237,2	MCF-7	breast:
7	chr10:1049476..1051729-chr10:1095238..1097700,2	K562	blood:

No data

Variant related genes	Relation type
GTPBP4	TF binding region
ENSG00000067064	Chromatin interaction
ENSG00000107937	Chromatin interaction
ENSG00000047056	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11253537	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11253538	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11253539	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11253540	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11253549	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11253550	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11253557	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11253558	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11253559	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11253560	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12356612	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12359796	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1250891	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12770173	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12771539	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12772979	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12773961	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12777788	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12777801	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17221456	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17221463	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17293580	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17293608	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1871621	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1871622	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34115136	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34480046	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35670857	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66462130	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7093665	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7094031	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	esv2753756	chr10:985264-1052950	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	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
18	esv1812809	chr10:1021156-1051728	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
19	esv1813158	chr10:1021156-1062915	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
20	esv1831483	chr10:1021156-1062915	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
21	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
22	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12770910	GTPBP4///IDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 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	chr10:1035800-1066200	Strong transcription	NH-A	brain
3	chr10:1036000-1066800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr10:1036200-1061800	Weak transcription	Stomach Mucosa	stomach
5	chr10:1036800-1066000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr10:1036800-1066800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr10:1036800-1066800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr10:1036800-1066800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:1037000-1066000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr10:1037000-1066200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr10:1037200-1066800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:1037200-1067200	Strong transcription	NHEK	skin
13	chr10:1037400-1053600	Strong transcription	K562	blood
14	chr10:1038000-1054000	Strong transcription	Hela-S3	cervix
15	chr10:1038000-1066200	Strong transcription	HUVEC	blood vessel
16	chr10:1038000-1066200	Strong transcription	Osteobl	bone
17	chr10:1038000-1067200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:1038200-1067000	Strong transcription	HSMM	muscle
19	chr10:1038200-1067200	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr10:1038200-1067400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr10:1038400-1063800	Strong transcription	HepG2	liver
22	chr10:1038400-1064200	Strong transcription	Brain Cingulate Gyrus	brain
23	chr10:1038400-1065600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr10:1038400-1065600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr10:1038400-1066000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr10:1038400-1066200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr10:1038400-1066200	Strong transcription	Stomach Smooth Muscle	stomach
28	chr10:1038400-1066800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr10:1038400-1066800	Strong transcription	HMEC	breast
30	chr10:1038600-1066200	Strong transcription	Brain Angular Gyrus	brain
31	chr10:1038600-1066800	Strong transcription	Fetal Thymus	thymus
32	chr10:1038600-1066800	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:1038600-1067000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr10:1038600-1067200	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr10:1038600-1068000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr10:1038800-1059600	Strong transcription	Lung	lung
37	chr10:1038800-1064200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr10:1038800-1064400	Strong transcription	Left Ventricle	heart
39	chr10:1038800-1065800	Strong transcription	Brain Anterior Caudate	brain
40	chr10:1038800-1066600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr10:1038800-1067000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr10:1038800-1067400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr10:1038800-1067800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr10:1039000-1060000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:1039000-1064200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr10:1040400-1053800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr10:1040600-1053400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr10:1040600-1058800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr10:1040600-1065600	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr10:1040800-1053200	Strong transcription	Colonic Mucosa	Colon

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