Variant report

Variant	rs66564457
Chromosome Location	chr3:47020072-47020073
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	POLR2A	chr3:47019959-47020130	K562	blood:	n/a	n/a
2	POLR2A	chr3:47019535-47020202	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47019120..47020713-chr3:47422216..47424593,2	K562	blood:
2	chr3:47019689..47022693-chr3:47040941..47043835,3	MCF-7	breast:
3	chr3:47019697..47022640-chr3:47324324..47326151,2	K562	blood:

Variant related genes	Relation type
NBEAL2	TF binding region
CCDC12	TF binding region
ENSG00000260236	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000160796	Chromatin interaction
ENSG00000114648	Chromatin interaction
ENSG00000076201	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10433549	0.85[EUR][1000 genomes]
rs10461018	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1079276	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1108301	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11130110	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130111	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130112	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11716553	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11720139	0.85[EUR][1000 genomes]
rs11917361	0.82[EUR][1000 genomes]
rs11917474	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12152493	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12491473	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12630534	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12715421	0.81[EUR][1000 genomes]
rs13062681	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066214	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13077398	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13091054	0.86[EUR][1000 genomes]
rs1463393	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17784127	0.82[EUR][1000 genomes]
rs1869869	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1869871	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2061197	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278963	0.86[EUR][1000 genomes]
rs2305634	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2305635	0.86[EUR][1000 genomes]
rs2305638	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2385867	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34103310	0.88[EUR][1000 genomes]
rs34344887	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4078466	0.84[EUR][1000 genomes]
rs4082155	0.85[EUR][1000 genomes]
rs4234465	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4682831	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4682837	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682844	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55724164	0.80[EUR][1000 genomes]
rs55843455	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56217494	0.82[EUR][1000 genomes]
rs56249396	0.81[EUR][1000 genomes]
rs61729713	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62246375	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246398	0.82[EUR][1000 genomes]
rs62248439	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66539935	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6763236	0.88[EUR][1000 genomes]
rs6767218	0.81[EUR][1000 genomes]
rs6774733	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6794193	0.87[EUR][1000 genomes]
rs6808742	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs749511	0.86[EUR][1000 genomes]
rs7610636	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7617689	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625067	0.88[EUR][1000 genomes]
rs7625070	0.88[EUR][1000 genomes]
rs7628747	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7633698	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636252	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7637302	0.85[EUR][1000 genomes]
rs7640397	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9858443	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
11	esv3492743	chr3:47019938-47020165	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	esv3374949	chr3:47019958-47020135	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	esv3381760	chr3:47019962-47020138	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	esv3359860	chr3:47019973-47022521	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	esv3463960	chr3:47019980-47020117	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	esv3492744	chr3:47019992-47020112	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	esv3463961	chr3:47019994-47020125	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
18	esv3492745	chr3:47019994-47020125	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47018200-47020600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:47018200-47020600	Weak transcription	Aorta	Aorta
3	chr3:47018200-47020600	Enhancers	Spleen	Spleen
4	chr3:47018400-47020400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:47018400-47020400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:47018400-47020400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:47018400-47020400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:47018400-47020400	Enhancers	Placenta	Placenta
9	chr3:47018400-47020400	Enhancers	Stomach Mucosa	stomach
10	chr3:47018400-47020600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:47018400-47020600	Weak transcription	HSMMtube	muscle
12	chr3:47018400-47020600	Enhancers	HUVEC	blood vessel
13	chr3:47018400-47020800	Weak transcription	Ovary	ovary
14	chr3:47018400-47021000	Flanking Active TSS	Dnd41	blood
15	chr3:47018600-47020400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:47018600-47020400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr3:47018600-47020400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:47018600-47020600	Weak transcription	Right Atrium	heart
19	chr3:47018800-47020200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr3:47018800-47020200	Enhancers	Primary B cells from peripheral blood	blood
21	chr3:47018800-47020400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr3:47018800-47020400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:47018800-47020400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:47018800-47020400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:47018800-47020400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:47018800-47020400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:47018800-47020400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:47018800-47020400	Enhancers	Primary B cells from cord blood	blood
29	chr3:47018800-47020400	Enhancers	Primary T cells from cord blood	blood
30	chr3:47018800-47020400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr3:47018800-47020400	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:47018800-47020400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:47018800-47020400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr3:47018800-47020400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:47018800-47020400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:47018800-47020400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:47018800-47020400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:47018800-47020400	Enhancers	Adipose Nuclei	Adipose
39	chr3:47018800-47020400	Enhancers	Liver	Liver
40	chr3:47018800-47020400	Enhancers	Brain Cingulate Gyrus	brain
41	chr3:47018800-47020400	Weak transcription	Brain Germinal Matrix	brain
42	chr3:47018800-47020400	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:47018800-47020400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:47018800-47020400	Enhancers	Colonic Mucosa	Colon
45	chr3:47018800-47020400	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr3:47018800-47020400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr3:47018800-47020400	Weak transcription	Fetal Brain Female	brain
48	chr3:47018800-47020400	Enhancers	Fetal Intestine Large	intestine
49	chr3:47018800-47020400	Enhancers	Fetal Intestine Small	intestine
50	chr3:47018800-47020400	Weak transcription	Fetal Kidney	kidney

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