Variant report

Variant	rs33964414
Chromosome Location	chr3:177396058-177396059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:177395868..177398215-chr3:177400550..177402752,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228561	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10513748	0.88[ASN][1000 genomes]
rs10513749	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10513750	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936953	0.82[ASN][1000 genomes]
rs10936954	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12487312	0.83[ASN][1000 genomes]
rs12487458	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489304	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489969	0.82[ASN][1000 genomes]
rs12490852	0.83[EUR][1000 genomes]
rs13059117	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13059514	0.82[ASN][1000 genomes]
rs13060224	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13060502	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13071785	0.83[ASN][1000 genomes]
rs13082519	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13097723	0.82[ASN][1000 genomes]
rs13340118	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13340167	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13340172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1499810	0.84[ASN][1000 genomes]
rs1500047	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1604032	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1846628	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2062499	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062500	0.83[ASN][1000 genomes]
rs28700961	0.81[ASN][1000 genomes]
rs28711160	0.81[ASN][1000 genomes]
rs34188001	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34491022	0.83[ASN][1000 genomes]
rs34992356	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35791913	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35847814	0.83[ASN][1000 genomes]
rs35868955	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4857725	0.82[ASN][1000 genomes]
rs4857726	0.82[ASN][1000 genomes]
rs56005554	0.82[ASN][1000 genomes]
rs57405296	0.99[ASN][1000 genomes]
rs62283347	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6443481	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6443482	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6765836	0.82[ASN][1000 genomes]
rs6772134	0.81[ASN][1000 genomes]
rs6779492	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793629	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793647	0.81[ASN][1000 genomes]
rs6798785	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6803889	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68151580	0.83[ASN][1000 genomes]
rs7610506	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615900	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7639373	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641099	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7644248	0.81[ASN][1000 genomes]
rs7646117	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7652174	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs937507	0.88[ASN][1000 genomes]
rs937561	0.84[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	esv2752972	chr3:176924298-177425298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv4131	chr3:177366549-177399301	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2590986	chr3:177395894-177397383	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177383800-177397800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:177391200-177397600	Weak transcription	Right Atrium	heart
3	chr3:177391600-177396400	Weak transcription	HUVEC	blood vessel
4	chr3:177391600-177396800	Weak transcription	Dnd41	blood
5	chr3:177391800-177397600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:177392000-177405400	Weak transcription	Brain Substantia Nigra	brain
7	chr3:177392200-177396800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:177392200-177397200	Weak transcription	HMEC	breast
9	chr3:177392200-177397200	Weak transcription	Osteobl	bone
10	chr3:177392200-177397400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:177392200-177397600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:177392200-177397600	Weak transcription	Adipose Nuclei	Adipose
13	chr3:177392200-177397800	Weak transcription	NHLF	lung
14	chr3:177392200-177404400	Weak transcription	Ovary	ovary
15	chr3:177392400-177396600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:177392400-177397200	Weak transcription	K562	blood
17	chr3:177392400-177397200	Weak transcription	NH-A	brain
18	chr3:177392400-177397400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:177392400-177397600	Weak transcription	NHDF-Ad	bronchial
20	chr3:177392400-177397800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:177392400-177418800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:177392600-177396200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:177392600-177396400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:177392600-177397400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:177392600-177397400	Weak transcription	Fetal Thymus	thymus
26	chr3:177392600-177397600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:177392600-177398600	Weak transcription	Spleen	Spleen
28	chr3:177392600-177399600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:177394000-177401000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:177394800-177404800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:177395000-177396600	Weak transcription	Fetal Heart	heart
32	chr3:177395000-177396800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:177395000-177396800	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:177395000-177397000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:177395000-177406000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:177395000-177411600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:177395200-177396400	Weak transcription	Fetal Kidney	kidney
38	chr3:177395200-177397000	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr3:177395200-177397400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:177395200-177399600	Weak transcription	Stomach Mucosa	stomach
41	chr3:177395200-177400200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:177395400-177399600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:177395400-177400200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:177395600-177397400	Weak transcription	Fetal Lung	lung
45	chr3:177395800-177396600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:177396000-177398600	Enhancers	Primary hematopoietic stem cells	blood
47	chr3:177396000-177401000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr3:177396000-177401200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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