Variant report

Variant	rs12777801
Chromosome Location	chr10:1036285-1036286
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:1035324-1036345	GM12878	blood:	n/a	n/a
2	RCOR1	chr10:1036269-1036304	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:1033990..1039615-chr10:1093691..1098446,7	MCF-7	breast:
2	chr10:974439..980732-chr10:1030011..1038533,28	MCF-7	breast:
3	chr10:976344..979673-chr10:1032747..1036349,14	K562	blood:
4	chr10:1033347..1035141-chr10:1035280..1036978,2	MCF-7	breast:
5	chr10:1003784..1006528-chr10:1035596..1037131,2	K562	blood:
6	chr10:1034471..1036574-chr10:1093266..1095946,3	K562	blood:
7	chr10:974636..980819-chr10:1029938..1037009,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000205740	TF binding region
ENSG00000067064	Chromatin interaction
ENSG00000229869	Chromatin interaction
ENSG00000047056	Chromatin interaction
ENSG00000107929	Chromatin interaction
ENSG00000107937	Chromatin interaction
ENSG00000205740	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1013504	1.00[ASN][1000 genomes]
rs10903358	1.00[ASN][1000 genomes]
rs11250228	1.00[CEU][hapmap]
rs11253504	1.00[ASN][1000 genomes]
rs11253518	1.00[ASN][1000 genomes]
rs11253530	1.00[ASN][1000 genomes]
rs11253537	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253538	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253539	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253540	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253549	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253550	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253557	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253558	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253559	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253560	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354914	1.00[ASN][1000 genomes]
rs12356612	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12357633	1.00[ASN][1000 genomes]
rs12359796	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250891	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761180	1.00[ASN][1000 genomes]
rs12762228	1.00[ASN][1000 genomes]
rs12768348	1.00[ASN][1000 genomes]
rs12769002	1.00[ASN][1000 genomes]
rs12770173	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12770910	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12771179	1.00[ASN][1000 genomes]
rs12771539	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12772979	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773961	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774985	1.00[ASN][1000 genomes]
rs12777021	1.00[ASN][1000 genomes]
rs12777788	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12777800	1.00[ASN][1000 genomes]
rs12778271	1.00[ASN][1000 genomes]
rs12781329	1.00[ASN][1000 genomes]
rs17221456	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17221463	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17221491	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs17293580	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17293608	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871621	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871622	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28512382	1.00[ASN][1000 genomes]
rs34115136	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34159706	1.00[ASN][1000 genomes]
rs34251037	1.00[ASN][1000 genomes]
rs34270668	1.00[ASN][1000 genomes]
rs34318754	1.00[ASN][1000 genomes]
rs34480046	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34487581	1.00[ASN][1000 genomes]
rs34527494	1.00[ASN][1000 genomes]
rs34885925	1.00[ASN][1000 genomes]
rs34982663	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]
rs35666723	1.00[ASN][1000 genomes]
rs35667562	1.00[ASN][1000 genomes]
rs35670857	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35709890	1.00[ASN][1000 genomes]
rs35957139	1.00[ASN][1000 genomes]
rs41260144	1.00[ASN][1000 genomes]
rs55697724	1.00[ASN][1000 genomes]
rs55708963	1.00[ASN][1000 genomes]
rs55742421	1.00[ASN][1000 genomes]
rs56222464	1.00[ASN][1000 genomes]
rs61830900	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	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66797613	1.00[ASN][1000 genomes]
rs67205460	1.00[ASN][1000 genomes]
rs67696450	1.00[ASN][1000 genomes]
rs7088956	1.00[ASN][1000 genomes]
rs7093665	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094031	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72778228	1.00[ASN][1000 genomes]
rs7914758	1.00[ASN][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
rs12777801	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	chr10:1035000-1037200	Enhancers	Small Intestine	intestine
2	chr10:1035000-1038800	Weak transcription	Aorta	Aorta
3	chr10:1035000-1094000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:1035200-1036400	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr10:1035200-1037200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr10:1035400-1036400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:1035400-1036800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr10:1035400-1036800	Enhancers	Pancreas	Pancrea
9	chr10:1035400-1039000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:1035400-1040000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:1035400-1040400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:1035600-1036400	Transcr. at gene 5' and 3'	NHEK	skin
13	chr10:1035600-1036800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr10:1035600-1036800	Weak transcription	Fetal Brain Female	brain
15	chr10:1035600-1037400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr10:1035600-1037400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr10:1035600-1038400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr10:1035600-1038800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr10:1035600-1039000	Weak transcription	Fetal Kidney	kidney
20	chr10:1035600-1043600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr10:1035800-1036800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr10:1035800-1036800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr10:1035800-1036800	Weak transcription	Gastric	stomach
24	chr10:1035800-1036800	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr10:1035800-1036800	Active TSS	GM12878-XiMat	blood
26	chr10:1035800-1036800	Enhancers	HUVEC	blood vessel
27	chr10:1035800-1037000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:1035800-1037200	Genic enhancers	Osteobl	bone
29	chr10:1035800-1038600	Weak transcription	Brain Angular Gyrus	brain
30	chr10:1035800-1038600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr10:1035800-1038600	Weak transcription	NHLF	lung
32	chr10:1035800-1038800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr10:1035800-1038800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr10:1035800-1038800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr10:1035800-1038800	Weak transcription	Brain Substantia Nigra	brain
36	chr10:1035800-1038800	Weak transcription	HSMMtube	muscle
37	chr10:1035800-1046800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr10:1035800-1066200	Strong transcription	NH-A	brain
39	chr10:1036000-1036400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr10:1036000-1036400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr10:1036000-1036400	Transcr. at gene 5' and 3'	A549	lung
42	chr10:1036000-1036600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr10:1036000-1036600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:1036000-1036600	Weak transcription	Fetal Lung	lung
45	chr10:1036000-1036600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr10:1036000-1036600	Enhancers	HepG2	liver
47	chr10:1036000-1036800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:1036000-1036800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr10:1036000-1036800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr10:1036000-1036800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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