Variant report

Variant	rs9839516
Chromosome Location	chr3:51681395-51681396
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	chr3:51680306..51681884-chr3:51703698..51705243,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164081	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs12330534	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13314120	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13321674	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13433729	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051799	0.85[AMR][1000 genomes]
rs17051832	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17081501	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28421789	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28452990	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28457212	0.85[AMR][1000 genomes]
rs28653367	0.85[AMR][1000 genomes]
rs2883900	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549265	0.85[AMR][1000 genomes]
rs56942057	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61737032	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951441	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953417	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953419	1.00[ASN][1000 genomes]
rs72953421	1.00[ASN][1000 genomes]
rs72953423	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953429	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7627636	1.00[ASN][1000 genomes]
rs904144	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9311470	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9808940	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9809757	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812008	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815684	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816075	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824779	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826664	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827665	0.85[AMR][1000 genomes]
rs9827917	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838294	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839608	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840331	0.85[AMR][1000 genomes]
rs9842066	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855809	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857893	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858497	0.85[AMR][1000 genomes]
rs9864213	0.85[AMR][1000 genomes]
rs9864952	1.00[ASN][1000 genomes]
rs9866513	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866604	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870147	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880050	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880909	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	0.85[AMR][1000 genomes]
rs9882601	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv997264	chr3:51584056-51689648	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536570	chr3:51584056-51689648	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv999553	chr3:51584056-51696052	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51660800-51681400	Strong transcription	Primary T cells from cord blood	blood
2	chr3:51660800-51681800	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:51660800-51683000	Strong transcription	Primary B cells from cord blood	blood
4	chr3:51660800-51683200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr3:51661000-51682600	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:51661000-51682600	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:51661000-51682600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:51661000-51683000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:51661000-51684200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:51661200-51681800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:51661200-51682600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:51661200-51683000	Strong transcription	Duodenum Mucosa	Duodenum
13	chr3:51661200-51683000	Strong transcription	Stomach Smooth Muscle	stomach
14	chr3:51661400-51681800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:51661400-51681800	Strong transcription	Lung	lung
16	chr3:51661400-51682600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:51661400-51682600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:51661400-51682800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:51661400-51683000	Strong transcription	Brain Hippocampus Middle	brain
20	chr3:51661600-51681600	Strong transcription	Fetal Stomach	stomach
21	chr3:51661600-51681800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr3:51661600-51682000	Strong transcription	Fetal Thymus	thymus
23	chr3:51661600-51682600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:51661600-51682600	Strong transcription	Brain Anterior Caudate	brain
25	chr3:51661600-51683200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr3:51661600-51683200	Strong transcription	Left Ventricle	heart
27	chr3:51661800-51683200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:51662000-51683000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:51662600-51681800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:51662600-51682600	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:51662800-51682400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr3:51663000-51682400	Strong transcription	Brain Substantia Nigra	brain
33	chr3:51663000-51682600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:51663000-51683000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:51663200-51682000	Strong transcription	Ovary	ovary
36	chr3:51663200-51682400	Strong transcription	Spleen	Spleen
37	chr3:51663200-51682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:51663200-51682800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:51664000-51683200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr3:51664800-51682400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:51667000-51682600	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr3:51667400-51681800	Strong transcription	Colon Smooth Muscle	Colon
43	chr3:51667400-51682200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:51667400-51683000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:51667400-51683200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:51667600-51682400	Strong transcription	Rectal Smooth Muscle	rectum
47	chr3:51667600-51682600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:51667600-51683000	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:51668800-51683200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:51669000-51681400	Strong transcription	HSMM	muscle

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