Variant report

Variant	rs2385869
Chromosome Location	chr3:46997248-46997249
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46988617..46992704-chr3:46994196..46998366,6	K562	blood:
2	chr3:46996489..46999843-chr3:47019877..47022356,3	MCF-7	breast:
3	chr3:46993041..46995087-chr3:46996208..46998631,3	K562	blood:
4	chr3:46983607..46987334-chr3:46993451..46998407,5	K562	blood:

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10461017	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10461019	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11130108	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs11130109	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11706212	1.00[AMR][1000 genomes]
rs11708257	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11709693	1.00[AMR][1000 genomes]
rs11709876	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11713537	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11928558	0.95[YRI][hapmap];1.00[AMR][1000 genomes]
rs12487763	0.89[AMR][1000 genomes]
rs12631730	0.95[YRI][hapmap]
rs13062185	1.00[AMR][1000 genomes]
rs13079416	0.89[AMR][1000 genomes]
rs13082531	1.00[AMR][1000 genomes]
rs13323092	0.91[YRI][hapmap]
rs1378818	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1463394	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1466272	0.89[AMR][1000 genomes]
rs1466273	0.89[AMR][1000 genomes]
rs1466274	0.89[AMR][1000 genomes]
rs1473382	0.89[AMR][1000 genomes]
rs1563431	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1814564	0.89[AMR][1000 genomes]
rs1869870	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2124509	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2124510	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2385868	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2891887	1.00[AMR][1000 genomes]
rs2891893	0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4018904	0.95[YRI][hapmap]
rs4282092	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4289375	0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs4324490	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4373094	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4378998	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4389512	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4450857	1.00[AMR][1000 genomes]
rs4478107	0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4522803	1.00[AMR][1000 genomes]
rs4525902	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4543047	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682828	0.89[AMR][1000 genomes]
rs4682832	0.86[YRI][hapmap];0.89[AMR][1000 genomes]
rs4682833	1.00[AMR][1000 genomes]
rs4682834	0.81[AFR][1000 genomes]
rs4682835	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682836	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4682838	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4682840	0.89[AMR][1000 genomes]
rs4682841	1.00[AMR][1000 genomes]
rs4682843	0.89[AMR][1000 genomes]
rs4683277	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683279	0.89[AMR][1000 genomes]
rs4683282	0.91[YRI][hapmap]
rs4683283	0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683284	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683285	0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683286	0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683289	0.89[AMR][1000 genomes]
rs4683290	0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683291	0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4683292	0.89[AMR][1000 genomes]
rs4683293	1.00[AMR][1000 genomes]
rs6442041	0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs6442042	0.84[YRI][hapmap];0.89[AMR][1000 genomes]
rs6442043	0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6442044	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6442047	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6442048	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6766676	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6768169	0.89[AMR][1000 genomes]
rs6775797	0.87[AMR][1000 genomes]
rs6780994	1.00[AMR][1000 genomes]
rs6785462	0.85[YRI][hapmap];0.89[AMR][1000 genomes]
rs6804732	0.89[AMR][1000 genomes]
rs6806521	0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6809904	0.88[YRI][hapmap];0.89[AMR][1000 genomes]
rs7621530	1.00[AMR][1000 genomes]
rs7624549	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7625011	0.91[YRI][hapmap];0.89[AMR][1000 genomes]
rs7630154	0.95[YRI][hapmap]
rs7630904	0.88[YRI][hapmap];0.89[AMR][1000 genomes]
rs7638549	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7643868	0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs7644382	0.91[YRI][hapmap]
rs7646076	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs7649941	0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7650142	0.86[YRI][hapmap];0.89[AMR][1000 genomes]
rs936177	0.88[YRI][hapmap];0.89[AMR][1000 genomes]
rs936178	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs936179	0.89[AMR][1000 genomes]
rs936180	0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs936181	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs936182	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs936186	0.96[YRI][hapmap];1.00[AMR][1000 genomes]
rs9810881	1.00[AMR][1000 genomes]
rs9812407	0.87[AMR][1000 genomes]
rs9828473	0.85[YRI][hapmap]
rs9862711	0.87[AMR][1000 genomes]
rs9878813	0.87[AMR][1000 genomes]
rs9883152	0.87[AMR][1000 genomes]
rs9990284	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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
4	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr3:46988000-47003200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:46989800-46998600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:46989800-47000600	Weak transcription	Brain Germinal Matrix	brain
6	chr3:46989800-47000600	Weak transcription	NHDF-Ad	bronchial
7	chr3:46989800-47001200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:46990000-47006800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:46990200-46998200	Weak transcription	Aorta	Aorta
10	chr3:46990200-47000800	Weak transcription	Fetal Brain Female	brain
11	chr3:46990400-47000000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr3:46991000-46998800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:46991000-47000200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:46991000-47001400	Weak transcription	Osteobl	bone
15	chr3:46991200-46997800	Weak transcription	Brain Angular Gyrus	brain
16	chr3:46991200-46997800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:46991200-46998000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:46991200-46998600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:46991200-46999600	Enhancers	A549	lung
20	chr3:46991200-47000000	Weak transcription	Fetal Lung	lung
21	chr3:46991200-47000200	Enhancers	Duodenum Mucosa	Duodenum
22	chr3:46991200-47000800	Weak transcription	Fetal Kidney	kidney
23	chr3:46991400-47000200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:46991400-47000400	Weak transcription	HMEC	breast
25	chr3:46991800-46997400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:46991800-46998600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:46992000-46998000	Enhancers	Fetal Muscle Leg	muscle
28	chr3:46992000-47001400	Weak transcription	NHLF	lung
29	chr3:46992400-46998600	Weak transcription	Hela-S3	cervix
30	chr3:46993000-46998400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:46993200-46999200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:46993200-46999200	Enhancers	Left Ventricle	heart
33	chr3:46993400-46998800	Enhancers	Spleen	Spleen
34	chr3:46993400-46999400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr3:46993400-47003600	Enhancers	Fetal Heart	heart
36	chr3:46993600-46998400	Genic enhancers	K562	blood
37	chr3:46993600-46999200	Enhancers	Adipose Nuclei	Adipose
38	chr3:46993600-46999200	Strong transcription	Fetal Stomach	stomach
39	chr3:46993600-46999200	Enhancers	Right Atrium	heart
40	chr3:46993600-47000000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr3:46993600-47003200	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr3:46994200-46997800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr3:46994200-46998800	Enhancers	Psoas Muscle	Psoas
44	chr3:46994200-46998800	Enhancers	Right Ventricle	heart
45	chr3:46994200-47001200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr3:46994200-47001600	Enhancers	Colon Smooth Muscle	Colon
47	chr3:46994200-47002200	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr3:46994200-47003200	Genic enhancers	Fetal Intestine Small	intestine
49	chr3:46994400-46998800	Enhancers	Esophagus	oesophagus
50	chr3:46994600-46998200	Enhancers	Rectal Mucosa Donor 29	rectum

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