Variant report

Variant	rs12706880
Chromosome Location	chr7:129041942-129041943
allele	A/G
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	EBF1	chr7:129041306-129042571	GM12878	blood:	n/a	chr7:129041567-129041580
2	PML	chr7:129041203-129042073	K562	blood:	n/a	chr7:129041484-129041493
3	GATA1	chr7:129041317-129042100	PBDE	blood:	n/a	chr7:129041954-129041961 chr7:129041954-129041963 chr7:129041954-129041961 chr7:129041950-129041961 chr7:129041947-129041968 chr7:129041953-129041963 chr7:129041954-129041961 chr7:129041489-129041496 chr7:129041950-129041966 chr7:129041952-129041965
4	RCOR1	chr7:129041206-129042466	K562	blood:	n/a	n/a
5	RCOR1	chr7:129041346-129041970	K562	blood:	n/a	n/a
6	JUN	chr7:129039870-129043044	K562	blood:	n/a	chr7:129041484-129041496 chr7:129041180-129041189 chr7:129041485-129041495 chr7:129041486-129041494
7	CUX1	chr7:129041267-129042422	K562	blood:	n/a	n/a
8	EP300	chr7:129041276-129041982	K562	blood:	n/a	n/a
9	CTCF	chr7:129041900-129042050	GM12871	blood:	n/a	n/a
10	TEAD4	chr7:129041116-129042506	K562	blood:	n/a	n/a
11	NR2F2	chr7:129041087-129042357	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:129039924..129043056-chr7:129049755..129051911,3	MCF-7	breast:
2	chr7:129041479..129044077-chr7:129074603..129076547,3	K562	blood:
3	chr7:129039765..129042733-chr7:129073588..129075374,2	MCF-7	breast:
4	chr7:129040377..129042656-chr7:129251574..129253363,2	K562	blood:
5	chr7:129041884..129042805-chr7:129111900..129112836,4	MCF-7	breast:
6	chr7:129040519..129043328-chr7:129251804..129254684,2	MCF-7	breast:
7	chr7:129041468..129043517-chr7:129074131..129076015,2	K562	blood:
8	chr7:129041500..129043384-chr7:129078242..129079753,2	K562	blood:
9	chr7:129041518..129042785-chr7:129111761..129112454,5	K562	blood:
10	chr7:129040687..129043309-chr7:129046318..129048641,3	K562	blood:

Variant related genes	Relation type
RNU7-16P	TF binding region
ENSG00000238072	Chromatin interaction
ENSG00000128578	Chromatin interaction
ENSG00000106459	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11766298	0.83[AMR][1000 genomes]
rs12706872	0.84[EUR][1000 genomes]
rs12706873	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12706874	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12706876	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12706877	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12706878	1.00[EUR][1000 genomes]
rs12706879	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12706881	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12706882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12706883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12706884	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13221770	0.84[EUR][1000 genomes]
rs13224964	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13225516	1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13226919	0.84[EUR][1000 genomes]
rs13230585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13235721	0.83[AMR][1000 genomes]
rs13240872	0.84[EUR][1000 genomes]
rs13242765	1.00[MEX][hapmap]
rs13245699	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13246455	1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34026893	0.84[EUR][1000 genomes]
rs34071868	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34285950	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34534484	0.84[EUR][1000 genomes]
rs34651338	0.84[EUR][1000 genomes]
rs34691806	0.84[EUR][1000 genomes]
rs34721141	0.84[EUR][1000 genomes]
rs34783919	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34822917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34867290	0.84[EUR][1000 genomes]
rs34890000	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35060087	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35064108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35120382	0.84[EUR][1000 genomes]
rs35195965	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35381790	0.84[EUR][1000 genomes]
rs35386880	0.84[EUR][1000 genomes]
rs35506900	0.84[EUR][1000 genomes]
rs35552948	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35654453	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35730873	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35866593	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35891284	0.84[EUR][1000 genomes]
rs36016296	0.84[EUR][1000 genomes]
rs36033343	0.84[EUR][1000 genomes]
rs36113794	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4338039	0.84[EUR][1000 genomes]
rs71577853	0.84[EUR][1000 genomes]
rs71577868	0.84[EUR][1000 genomes]
rs71577869	0.84[EUR][1000 genomes]
rs71577875	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71579838	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71579847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71579850	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71579851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71579852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71579854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71579855	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525482	chr7:128890812-129045191	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv3331483	chr7:128918442-129082887	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1015550	chr7:128992460-129111060	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv539122	chr7:128992460-129111060	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128989200-129044200	Weak transcription	Ovary	ovary
2	chr7:129006200-129046000	Weak transcription	Aorta	Aorta
3	chr7:129008400-129044200	Weak transcription	Fetal Muscle Leg	muscle
4	chr7:129008400-129073200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:129015800-129053400	Weak transcription	Fetal Lung	lung
6	chr7:129016000-129062400	Weak transcription	Pancreas	Pancrea
7	chr7:129016000-129071400	Weak transcription	Small Intestine	intestine
8	chr7:129016400-129052400	Weak transcription	Fetal Kidney	kidney
9	chr7:129016600-129055200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:129017400-129051800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:129017400-129069200	Weak transcription	Stomach Mucosa	stomach
12	chr7:129017400-129073000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr7:129017800-129064600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr7:129018400-129070000	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:129019400-129070800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:129019800-129066200	Weak transcription	Thymus	Thymus
17	chr7:129020000-129064600	Weak transcription	Spleen	Spleen
18	chr7:129023000-129047800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr7:129025600-129046200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:129025800-129042400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:129026800-129060600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr7:129027800-129044400	Weak transcription	Dnd41	blood
23	chr7:129027800-129070200	Weak transcription	HepG2	liver
24	chr7:129028400-129042000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr7:129028400-129063800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr7:129028400-129073000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:129028800-129042600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:129028800-129044600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr7:129028800-129047400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr7:129029000-129070000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:129029200-129073200	Weak transcription	Brain Angular Gyrus	brain
32	chr7:129029600-129067400	Weak transcription	Fetal Brain Male	brain
33	chr7:129029800-129047600	Weak transcription	Brain Germinal Matrix	brain
34	chr7:129029800-129052200	Weak transcription	Fetal Brain Female	brain
35	chr7:129030600-129042600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr7:129030600-129043000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:129030800-129043600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:129031000-129048800	Weak transcription	Fetal Thymus	thymus
39	chr7:129031200-129042000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr7:129031200-129042400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr7:129032400-129043800	Weak transcription	Colonic Mucosa	Colon
42	chr7:129033800-129073600	Weak transcription	Right Ventricle	heart
43	chr7:129034200-129066200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:129035400-129043200	Weak transcription	Brain Hippocampus Middle	brain
45	chr7:129035400-129053800	Weak transcription	Brain Substantia Nigra	brain
46	chr7:129035600-129042200	Weak transcription	Right Atrium	heart
47	chr7:129035600-129046200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:129035600-129053400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:129035600-129062000	Weak transcription	Left Ventricle	heart
50	chr7:129035600-129072600	Weak transcription	H9 Cell Line	embryonic stem cell

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