Variant report

Variant	rs66539935
Chromosome Location	chr3:47025327-47025328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46988383..46991103-chr3:47025292..47027507,2	MCF-7	breast:
2	chr3:46976166..46978368-chr3:47023917..47025847,2	MCF-7	breast:
3	chr3:46974856..46983636-chr3:47025231..47032249,9	K562	blood:
4	chr3:46990736..46992416-chr3:47023933..47026692,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10433549	0.87[EUR][1000 genomes]
rs10461018	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1079276	0.96[EUR][1000 genomes]
rs1108301	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130110	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11130111	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11130112	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707736	0.80[EUR][1000 genomes]
rs11709660	0.81[EUR][1000 genomes]
rs11715121	0.81[EUR][1000 genomes]
rs11716553	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11720139	0.88[EUR][1000 genomes]
rs11917361	0.83[EUR][1000 genomes]
rs11917474	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12152493	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12491473	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12630534	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12715421	0.82[EUR][1000 genomes]
rs13062681	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13066214	0.96[EUR][1000 genomes]
rs13077398	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13091054	0.87[EUR][1000 genomes]
rs1463393	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17784127	0.85[EUR][1000 genomes]
rs1869869	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1869871	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2061197	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2278963	0.88[EUR][1000 genomes]
rs2305634	0.96[EUR][1000 genomes]
rs2305635	0.88[EUR][1000 genomes]
rs2305638	0.91[EUR][1000 genomes]
rs2385867	0.93[EUR][1000 genomes]
rs34103310	0.89[EUR][1000 genomes]
rs34344887	0.95[EUR][1000 genomes]
rs4078466	0.85[EUR][1000 genomes]
rs4082155	0.85[EUR][1000 genomes]
rs4234465	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682831	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682837	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4682844	0.95[EUR][1000 genomes]
rs4683322	0.81[EUR][1000 genomes]
rs55724164	0.83[EUR][1000 genomes]
rs55843455	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55927279	0.82[EUR][1000 genomes]
rs56217494	0.85[EUR][1000 genomes]
rs56249396	0.83[EUR][1000 genomes]
rs61729713	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62246375	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62246398	0.83[EUR][1000 genomes]
rs62248439	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6442055	0.81[EUR][1000 genomes]
rs66564457	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6763236	0.88[EUR][1000 genomes]
rs6767218	0.83[EUR][1000 genomes]
rs6768722	0.81[EUR][1000 genomes]
rs6774733	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6777145	0.81[EUR][1000 genomes]
rs6794193	0.87[EUR][1000 genomes]
rs6808742	0.91[EUR][1000 genomes]
rs749511	0.88[EUR][1000 genomes]
rs7610636	0.92[EUR][1000 genomes]
rs7617689	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7625067	0.89[EUR][1000 genomes]
rs7625070	0.89[EUR][1000 genomes]
rs7628747	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7633698	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7636252	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7637302	0.86[EUR][1000 genomes]
rs7640397	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9844122	0.80[EUR][1000 genomes]
rs9845728	0.80[EUR][1000 genomes]
rs9854790	0.81[EUR][1000 genomes]
rs9858443	0.82[EUR][1000 genomes]
rs9875235	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47021800-47028400	Weak transcription	Small Intestine	intestine
2	chr3:47021800-47036000	Weak transcription	Ovary	ovary
3	chr3:47022000-47025400	Enhancers	Placenta	Placenta
4	chr3:47022000-47025400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr3:47022000-47030200	Weak transcription	Aorta	Aorta
6	chr3:47022200-47030200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:47022400-47026600	Enhancers	K562	blood
8	chr3:47022400-47028800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:47022400-47029600	Weak transcription	Liver	Liver
10	chr3:47022400-47039800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:47022400-47041600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:47022400-47041800	Weak transcription	Brain Germinal Matrix	brain
13	chr3:47022400-47042000	Weak transcription	Brain Substantia Nigra	brain
14	chr3:47022600-47025400	Enhancers	Lung	lung
15	chr3:47022600-47027800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr3:47022600-47028200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:47022600-47028200	Weak transcription	Fetal Heart	heart
18	chr3:47022600-47028400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:47022600-47028600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:47022600-47028600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:47022600-47049000	Weak transcription	Hela-S3	cervix
22	chr3:47022600-47050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:47023200-47042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:47023400-47026000	Weak transcription	Fetal Kidney	kidney
25	chr3:47023400-47028400	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:47023600-47025400	Enhancers	Gastric	stomach
27	chr3:47023600-47025400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr3:47023600-47025600	Enhancers	GM12878-XiMat	blood
29	chr3:47023600-47025800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:47023600-47028200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:47023600-47028200	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:47023600-47028600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:47023600-47028800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:47023600-47035600	Weak transcription	Brain Anterior Caudate	brain
35	chr3:47023800-47025600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:47023800-47025800	Weak transcription	Fetal Stomach	stomach
37	chr3:47023800-47026000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:47023800-47026000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr3:47023800-47026200	Weak transcription	Thymus	Thymus
40	chr3:47023800-47026600	Weak transcription	Right Ventricle	heart
41	chr3:47023800-47026800	Weak transcription	Right Atrium	heart
42	chr3:47023800-47027600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:47023800-47027600	Weak transcription	A549	lung
44	chr3:47023800-47028000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:47023800-47028200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:47023800-47028200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:47023800-47028400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:47023800-47028400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:47023800-47028400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:47023800-47029000	Weak transcription	Rectal Smooth Muscle	rectum

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