Variant report

Variant	rs939851
Chromosome Location	chr3:20127751-20127752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:20114096..20116899-chr3:20125846..20128363,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11128936	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714203	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636325	0.82[EUR][1000 genomes]
rs12639358	0.84[EUR][1000 genomes]
rs1879775	0.84[EUR][1000 genomes]
rs2293139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365362	0.84[EUR][1000 genomes]
rs2365370	0.84[EUR][1000 genomes]
rs2365371	0.84[EUR][1000 genomes]
rs2365793	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2623075	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2661377	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2661379	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2929399	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2929400	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2929403	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2929405	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2948083	0.85[EUR][1000 genomes]
rs2948086	0.85[EUR][1000 genomes]
rs2948087	0.85[EUR][1000 genomes]
rs2948088	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60355368	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6779759	0.86[EUR][1000 genomes]
rs6784715	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7623123	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	15 gene(s)	inside rSNPs	diseases
5	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
13	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
14	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
15	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20102800-20136800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:20106800-20130800	Weak transcription	Fetal Intestine Large	intestine
3	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
4	chr3:20117200-20130800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr3:20118800-20129200	Weak transcription	Fetal Lung	lung
6	chr3:20122800-20131000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:20123000-20127800	Weak transcription	Right Atrium	heart
8	chr3:20123000-20131000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:20123000-20131600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:20123000-20137000	Weak transcription	Spleen	Spleen
11	chr3:20123000-20138400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:20123000-20140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:20123000-20153000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:20123200-20129400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:20123200-20129400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:20123200-20129400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:20123200-20130200	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:20123200-20131000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:20123200-20131000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:20123200-20131000	Weak transcription	Adipose Nuclei	Adipose
21	chr3:20123200-20131000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:20123200-20131000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:20123200-20131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:20123200-20131200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:20123200-20131200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:20123200-20131600	Weak transcription	Brain Substantia Nigra	brain
27	chr3:20123200-20132400	Weak transcription	Liver	Liver
28	chr3:20123200-20132800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:20123200-20136800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:20123200-20136800	Weak transcription	Brain Angular Gyrus	brain
31	chr3:20123200-20136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:20123200-20137000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:20123200-20137200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:20123200-20137200	Weak transcription	Esophagus	oesophagus
35	chr3:20123200-20137200	Weak transcription	Fetal Heart	heart
36	chr3:20123200-20137200	Weak transcription	Left Ventricle	heart
37	chr3:20123200-20137200	Weak transcription	Psoas Muscle	Psoas
38	chr3:20123200-20137200	Weak transcription	Right Ventricle	heart
39	chr3:20123200-20137400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:20123200-20137400	Weak transcription	Gastric	stomach
41	chr3:20123200-20137400	Weak transcription	Pancreas	Pancrea
42	chr3:20123200-20138600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:20123200-20141000	Weak transcription	Stomach Mucosa	stomach
44	chr3:20123200-20153200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:20125400-20129200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:20126000-20131000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:20126400-20128600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:20126800-20128400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:20127000-20128200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:20127000-20128200	Strong transcription	Fetal Stomach	stomach

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