Variant report

Variant	rs41260144
Chromosome Location	chr10:1065406-1065407
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:1065326-1065662	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:1065054-1066219	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:1064919-1065899	GM12892	blood:	n/a	n/a
4	POLR2A	chr10:1065306-1065699	GM12878	blood:	n/a	n/a
5	POLR2A	chr10:1064806-1065893	GM12878	blood:	n/a	n/a
6	POLR2A	chr10:1064859-1065769	K562	blood:	n/a	n/a
7	POLR2A	chr10:1065359-1065699	GM12878	blood:	n/a	n/a
8	POLR2A	chr10:1064640-1065867	GM12891	blood:	n/a	n/a
9	POLR2A	chr10:1065244-1065702	U87	brain:	n/a	n/a
10	POLR2A	chr10:1064809-1065761	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr10:1064992-1065760	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr10:1064487-1066229	GM12892	blood:	n/a	n/a
13	POLR2A	chr10:1065001-1065633	HepG2	liver:	n/a	n/a
14	POLR2A	chr10:1064657-1066260	GM12892	blood:	n/a	n/a
15	POLR2A	chr10:1064798-1065736	K562	blood:	n/a	n/a
16	POLR2A	chr10:1064972-1065756	K562	blood:	n/a	n/a
17	POLR2A	chr10:1065320-1065559	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr10:1065310-1065718	GM12878	blood:	n/a	n/a
19	POLR2A	chr10:1065001-1065755	GM19193	blood:	n/a	n/a
20	PML	chr10:1065197-1065827	K562	blood:	n/a	n/a
21	TEAD4	chr10:1065051-1065565	K562	blood:	n/a	n/a
22	POLR2A	chr10:1065265-1065699	HL-60	blood:	n/a	n/a
23	POLR2A	chr10:1065029-1067893	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr10:1065282-1065796	GM12891	blood:	n/a	n/a
25	POLR2A	chr10:1064828-1067879	K562	blood:	n/a	n/a
26	POLR2A	chr10:1065072-1066137	K562	blood:	n/a	n/a
27	POLR2A	chr10:1065284-1065794	HepG2	liver:	n/a	n/a
28	POLR2A	chr10:1065406-1065513	MCF-7	breast:	n/a	n/a
29	POLR2A	chr10:1065001-1066175	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr10:1065359-1065653	MCF-7	breast:	n/a	n/a
31	POLR2A	chr10:1064818-1065837	K562	blood:	n/a	n/a
32	BCLAF1	chr10:1065120-1065685	GM12878	blood:	n/a	n/a
33	POLR2A	chr10:1065339-1065724	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr10:1065280-1065709	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr10:1064706-1065855	GM12891	blood:	n/a	n/a
36	POLR2A	chr10:1065358-1065475	A549	lung:	n/a	n/a
37	NFATC1	chr10:1065276-1065981	GM12878	blood:	n/a	n/a
38	POLR2A	chr10:1064885-1066160	GM12891	blood:	n/a	n/a
39	POLR2A	chr10:1065385-1066271	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr10:1064920-1067522	K562	blood:	n/a	n/a
41	POLR2A	chr10:1065276-1065801	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr10:1064830-1066186	HepG2	liver:	n/a	n/a
43	POLR2A	chr10:1064682-1066138	GM12891	blood:	n/a	n/a
44	POLR2A	chr10:1065050-1066069	IMR90	lung:	n/a	n/a
45	POLR2A	chr10:1065312-1065545	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr10:1064790-1067937	A549	lung:	n/a	n/a
47	POLR2A	chr10:1065025-1065812	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr10:1065339-1065532	A549	lung:	n/a	n/a
49	POLR2A	chr10:1064670-1065866	GM12892	blood:	n/a	n/a
50	POLR2A	chr10:1065287-1065580	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:1061106..1063843-chr10:1063922..1066024,3	K562	blood:
2	chr10:1057974..1060737-chr10:1065282..1067560,6	K562	blood:
3	chr10:1039567..1041272-chr10:1064973..1067031,2	K562	blood:

No data

Variant related genes	Relation type
IDI2-AS1	TF binding region
ENSG00000107937	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1013504	1.00[ASN][1000 genomes]
rs10508206	0.86[EUR][1000 genomes]
rs10903358	1.00[ASN][1000 genomes]
rs11250228	0.86[EUR][1000 genomes]
rs11253504	1.00[ASN][1000 genomes]
rs11253518	1.00[ASN][1000 genomes]
rs11253530	1.00[ASN][1000 genomes]
rs11253537	1.00[ASN][1000 genomes]
rs11253538	1.00[ASN][1000 genomes]
rs11253539	1.00[ASN][1000 genomes]
rs11253540	1.00[ASN][1000 genomes]
rs11253549	1.00[ASN][1000 genomes]
rs11253550	1.00[ASN][1000 genomes]
rs11253557	1.00[ASN][1000 genomes]
rs11253558	1.00[ASN][1000 genomes]
rs11253559	1.00[ASN][1000 genomes]
rs11253560	1.00[ASN][1000 genomes]
rs12354914	1.00[ASN][1000 genomes]
rs12356612	1.00[ASN][1000 genomes]
rs12357633	1.00[ASN][1000 genomes]
rs12359796	1.00[ASN][1000 genomes]
rs1250891	1.00[ASN][1000 genomes]
rs12762228	1.00[ASN][1000 genomes]
rs12762955	0.85[EUR][1000 genomes]
rs12768348	1.00[ASN][1000 genomes]
rs12769002	1.00[ASN][1000 genomes]
rs12770173	1.00[ASN][1000 genomes]
rs12771539	1.00[ASN][1000 genomes]
rs12772979	1.00[ASN][1000 genomes]
rs12773961	1.00[ASN][1000 genomes]
rs12774985	1.00[ASN][1000 genomes]
rs12777021	1.00[ASN][1000 genomes]
rs12777800	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12777801	1.00[ASN][1000 genomes]
rs12778271	1.00[ASN][1000 genomes]
rs12781329	1.00[ASN][1000 genomes]
rs12783621	0.82[EUR][1000 genomes]
rs12784928	0.82[EUR][1000 genomes]
rs17221456	1.00[ASN][1000 genomes]
rs17221463	1.00[ASN][1000 genomes]
rs17221491	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17293580	1.00[ASN][1000 genomes]
rs17293608	1.00[ASN][1000 genomes]
rs1871621	1.00[ASN][1000 genomes]
rs1871622	1.00[ASN][1000 genomes]
rs28512382	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34115136	1.00[ASN][1000 genomes]
rs34159706	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34270668	1.00[ASN][1000 genomes]
rs34318754	1.00[ASN][1000 genomes]
rs34480046	1.00[ASN][1000 genomes]
rs34487581	1.00[ASN][1000 genomes]
rs34527494	1.00[ASN][1000 genomes]
rs34884971	0.86[EUR][1000 genomes]
rs34885925	1.00[ASN][1000 genomes]
rs35028518	1.00[ASN][1000 genomes]
rs35306767	1.00[ASN][1000 genomes]
rs35363972	1.00[ASN][1000 genomes]
rs35443149	1.00[ASN][1000 genomes]
rs35667562	1.00[ASN][1000 genomes]
rs35670857	1.00[ASN][1000 genomes]
rs35709890	1.00[ASN][1000 genomes]
rs35957139	1.00[ASN][1000 genomes]
rs55697724	1.00[ASN][1000 genomes]
rs55708963	1.00[ASN][1000 genomes]
rs55742421	1.00[ASN][1000 genomes]
rs61830926	1.00[ASN][1000 genomes]
rs61830931	1.00[ASN][1000 genomes]
rs61830933	1.00[ASN][1000 genomes]
rs61833260	1.00[ASN][1000 genomes]
rs61833265	1.00[ASN][1000 genomes]
rs66462130	1.00[ASN][1000 genomes]
rs66797613	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67205460	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67696450	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7088956	1.00[ASN][1000 genomes]
rs7093665	1.00[ASN][1000 genomes]
rs7094031	1.00[ASN][1000 genomes]
rs71491334	0.84[EUR][1000 genomes]
rs72778228	1.00[ASN][1000 genomes]
rs7914758	1.00[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
rs41260144	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	chr10:1036800-1066000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr10:1036800-1066800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr10:1036800-1066800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr10:1036800-1066800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:1037000-1066000	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr10:1037000-1066200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr10:1037200-1066800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:1037200-1067200	Strong transcription	NHEK	skin
12	chr10:1038000-1066200	Strong transcription	HUVEC	blood vessel
13	chr10:1038000-1066200	Strong transcription	Osteobl	bone
14	chr10:1038000-1067200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:1038200-1067000	Strong transcription	HSMM	muscle
16	chr10:1038200-1067200	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr10:1038200-1067400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr10:1038400-1065600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr10:1038400-1065600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr10:1038400-1066000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr10:1038400-1066200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr10:1038400-1066200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr10:1038400-1066800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:1038400-1066800	Strong transcription	HMEC	breast
25	chr10:1038600-1066200	Strong transcription	Brain Angular Gyrus	brain
26	chr10:1038600-1066800	Strong transcription	Fetal Thymus	thymus
27	chr10:1038600-1066800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr10:1038600-1067000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr10:1038600-1067200	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr10:1038600-1068000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:1038800-1065800	Strong transcription	Brain Anterior Caudate	brain
32	chr10:1038800-1066600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr10:1038800-1067000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr10:1038800-1067400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:1038800-1067800	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr10:1040600-1065600	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr10:1041200-1067800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr10:1046400-1066000	Strong transcription	HSMMtube	muscle
39	chr10:1046800-1068600	Weak transcription	Right Atrium	heart
40	chr10:1047600-1067400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr10:1048200-1066200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr10:1048200-1066800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr10:1048200-1066800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr10:1048600-1066800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:1048600-1067200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr10:1048800-1067200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr10:1049000-1066200	Strong transcription	Liver	Liver
48	chr10:1049000-1066600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr10:1049000-1066800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr10:1049000-1066800	Strong transcription	Primary T cells from cord blood	blood

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