Variant report

Variant	rs6852282
Chromosome Location	chr4:102256843-102256844
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	chr4:102254449..102259198-chr4:102265596..102269977,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138814	Chromatin interaction
ENSG00000254531	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1011849	0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11943655	0.91[AMR][1000 genomes]
rs11946103	0.91[AMR][1000 genomes]
rs1372243	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1372244	0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1441431	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1441434	0.91[AMR][1000 genomes]
rs1561722	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs17031168	0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031172	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031175	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031176	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031180	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17031182	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3789755	0.81[AFR][1000 genomes]
rs3974659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4488940	0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4504259	0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4637408	0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs55667372	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58629361	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59079781	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59224049	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59763039	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60438397	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60984918	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6532924	0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6532925	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6532926	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6810812	0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6812094	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6817805	0.82[AFR][1000 genomes]
rs6827528	0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6828025	0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6830390	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6831471	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6831824	0.82[AFR][1000 genomes]
rs6832020	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6834721	0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6837858	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6842191	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6844844	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6846554	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835916	0.91[AMR][1000 genomes]
rs73835923	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835924	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835931	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835932	0.83[AMR][1000 genomes]
rs73835933	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835934	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835935	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835936	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835939	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835940	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835941	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835943	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835944	0.82[AFR][1000 genomes]
rs7655806	0.91[AMR][1000 genomes]
rs7661895	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7664396	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7671524	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102244000-102258000	Weak transcription	Brain Angular Gyrus	brain
2	chr4:102249600-102266400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:102250200-102258200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:102250200-102265200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:102250400-102265800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr4:102250600-102266000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:102251000-102258200	Weak transcription	Dnd41	blood
8	chr4:102251000-102260200	Weak transcription	Brain Anterior Caudate	brain
9	chr4:102251200-102258000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:102251200-102259600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:102251200-102265800	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:102252000-102258000	Weak transcription	Primary T cells from cord blood	blood
13	chr4:102252000-102265800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:102252200-102258400	Weak transcription	Osteobl	bone
15	chr4:102252200-102266000	Weak transcription	Fetal Lung	lung
16	chr4:102252600-102258000	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:102252600-102258600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:102252800-102266400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:102253000-102257800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:102253200-102258800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:102253400-102258400	Weak transcription	NHEK	skin
22	chr4:102253400-102258800	Weak transcription	A549	lung
23	chr4:102253800-102258600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:102254000-102266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:102255000-102257000	Enhancers	Ovary	ovary
26	chr4:102255000-102257200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr4:102255200-102258000	Weak transcription	Primary B cells from cord blood	blood
28	chr4:102255200-102266400	Weak transcription	Gastric	stomach
29	chr4:102255400-102257000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:102255400-102266600	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:102255800-102257000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:102255800-102257000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr4:102255800-102257000	Enhancers	Small Intestine	intestine
34	chr4:102256000-102257000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:102256000-102257000	Enhancers	Fetal Heart	heart
36	chr4:102256000-102257000	Enhancers	Stomach Mucosa	stomach
37	chr4:102256000-102259600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr4:102256200-102257000	Enhancers	Primary B cells from peripheral blood	blood
39	chr4:102256200-102257000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:102256200-102257000	Enhancers	Fetal Brain Female	brain
41	chr4:102256200-102257000	Enhancers	Right Ventricle	heart
42	chr4:102256200-102257000	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr4:102256200-102257000	Flanking Active TSS	GM12878-XiMat	blood
44	chr4:102256200-102257200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:102256400-102257000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr4:102256400-102257000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:102256400-102257000	Enhancers	Left Ventricle	heart
48	chr4:102256400-102257000	Enhancers	Lung	lung
49	chr4:102256400-102257000	Enhancers	Pancreas	Pancrea
50	chr4:102256400-102257000	Enhancers	Right Atrium	heart

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