Variant report

Variant	rs11706212
Chromosome Location	chr3:47024362-47024363
allele	A/T
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	POLR2A	chr3:47023365-47024820	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46976166..46978368-chr3:47023917..47025847,2	MCF-7	breast:
2	chr3:46990736..46992416-chr3:47023933..47026692,2	K562	blood:
3	chr3:47022327..47024798-chr3:47034790..47037154,3	MCF-7	breast:

Variant related genes	Relation type
CCDC12	TF binding region
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 164 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs10461017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10461019	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs11130108	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11130109	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11708257	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709876	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713537	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12487763	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs13062185	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13062516	0.96[AFR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13079416	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13082531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1378818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1463394	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466272	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466273	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466274	0.89[AMR][1000 genomes]
rs1473382	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473384	1.00[EUR][1000 genomes]
rs1473385	1.00[EUR][1000 genomes]
rs1563431	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1563432	1.00[EUR][1000 genomes]
rs1814564	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1869870	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2124509	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124510	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs2385863	1.00[EUR][1000 genomes]
rs2385868	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2385869	1.00[AMR][1000 genomes]
rs2385872	0.88[AFR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs2891887	1.00[AMR][1000 genomes]
rs2891893	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs35366910	1.00[EUR][1000 genomes]
rs4018904	1.00[EUR][1000 genomes]
rs4282092	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4289375	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4324490	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4373094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4378998	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4389512	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4450857	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4478107	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4522803	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4525902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4543047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682828	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682832	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682833	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682834	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4682835	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682836	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682838	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682840	0.89[AMR][1000 genomes]
rs4682841	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682843	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682846	1.00[EUR][1000 genomes]
rs4682847	1.00[EUR][1000 genomes]
rs4683277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683279	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683283	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683284	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683285	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683286	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683292	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4683303	1.00[EUR][1000 genomes]
rs6442041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442042	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442043	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442044	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442048	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442050	0.84[AFR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6766676	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6768169	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6772449	1.00[EUR][1000 genomes]
rs6775797	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6778687	1.00[EUR][1000 genomes]
rs6780994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6785462	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787210	1.00[EUR][1000 genomes]
rs6804732	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806521	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808052	1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs6809904	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624549	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7625011	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7630904	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7631423	0.83[AFR][1000 genomes]
rs7638549	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7639121	1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7643868	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7644382	1.00[EUR][1000 genomes]
rs7646076	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	1.00[EUR][1000 genomes]
rs7649941	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650142	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs936173	1.00[EUR][1000 genomes]
rs936177	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936178	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936179	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936180	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936181	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936182	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9810881	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9812407	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9819344	1.00[EUR][1000 genomes]
rs9819475	1.00[EUR][1000 genomes]
rs9823480	1.00[EUR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9827293	1.00[EUR][1000 genomes]
rs9828473	1.00[EUR][1000 genomes]
rs9833500	1.00[EUR][1000 genomes]
rs9836801	1.00[EUR][1000 genomes]
rs9850151	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9862711	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]
rs9878813	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9883152	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9883909	1.00[EUR][1000 genomes]
rs9990284	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription 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	28 gene(s)	inside rSNPs	diseases
6	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
8	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47021600-47024600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr3:47021800-47024400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr3:47021800-47028400	Weak transcription	Small Intestine	intestine
4	chr3:47021800-47036000	Weak transcription	Ovary	ovary
5	chr3:47022000-47024400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:47022000-47024400	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr3:47022000-47024600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:47022000-47025400	Enhancers	Placenta	Placenta
9	chr3:47022000-47025400	Enhancers	Placenta Amnion	Placenta Amnion
10	chr3:47022000-47030200	Weak transcription	Aorta	Aorta
11	chr3:47022200-47024400	Enhancers	HepG2	liver
12	chr3:47022200-47030200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:47022400-47024400	Enhancers	Primary B cells from peripheral blood	blood
14	chr3:47022400-47024400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:47022400-47024600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:47022400-47024600	Enhancers	Fetal Lung	lung
17	chr3:47022400-47026600	Enhancers	K562	blood
18	chr3:47022400-47028800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:47022400-47029600	Weak transcription	Liver	Liver
20	chr3:47022400-47039800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:47022400-47041600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:47022400-47041800	Weak transcription	Brain Germinal Matrix	brain
23	chr3:47022400-47042000	Weak transcription	Brain Substantia Nigra	brain
24	chr3:47022600-47024400	Enhancers	Fetal Intestine Large	intestine
25	chr3:47022600-47024600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:47022600-47024800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:47022600-47025400	Enhancers	Lung	lung
28	chr3:47022600-47027800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr3:47022600-47028200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:47022600-47028200	Weak transcription	Fetal Heart	heart
31	chr3:47022600-47028400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr3:47022600-47028600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr3:47022600-47028600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:47022600-47049000	Weak transcription	Hela-S3	cervix
35	chr3:47022600-47050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:47023000-47024400	Flanking Active TSS	Stomach Mucosa	stomach
37	chr3:47023200-47042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:47023400-47024800	Enhancers	Primary B cells from cord blood	blood
39	chr3:47023400-47026000	Weak transcription	Fetal Kidney	kidney
40	chr3:47023400-47028400	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:47023600-47024400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:47023600-47025000	Enhancers	Fetal Thymus	thymus
43	chr3:47023600-47025400	Enhancers	Gastric	stomach
44	chr3:47023600-47025400	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr3:47023600-47025600	Enhancers	GM12878-XiMat	blood
46	chr3:47023600-47025800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:47023600-47028200	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr3:47023600-47028200	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:47023600-47028600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr3:47023600-47028800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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