Variant report

Variant	rs6846554
Chromosome Location	chr4:102226267-102226268
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102226021..102228958-chr4:102267685..102270990,3	MCF-7	breast:
2	chr4:102219978..102222828-chr4:102224431..102227610,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254531	Chromatin interaction
ENSG00000138814	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1011849	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11943655	0.91[AMR][1000 genomes]
rs11946103	0.91[AMR][1000 genomes]
rs1372243	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1372244	0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1441431	0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1441434	0.91[AMR][1000 genomes]
rs1561722	0.84[YRI][hapmap];0.92[AFR][1000 genomes]
rs17031168	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031172	0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031175	0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031176	0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031180	0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17031182	0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3789755	0.86[AFR][1000 genomes]
rs3974659	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4488940	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4504259	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4637408	0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs55667372	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58629361	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59079781	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59224049	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59763039	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60438397	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60984918	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6532924	0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6532925	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6532926	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6810812	0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6812094	0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6817805	0.87[AFR][1000 genomes]
rs6827528	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6828025	0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6830390	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6831471	0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6831824	0.87[AFR][1000 genomes]
rs6832020	0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6834721	0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6837858	0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6842191	0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6844844	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6852282	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835916	0.91[AMR][1000 genomes]
rs73835923	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835924	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835931	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835932	0.83[AMR][1000 genomes]
rs73835933	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835934	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835935	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835936	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835937	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835938	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835939	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835940	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835941	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835943	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7655806	0.91[AMR][1000 genomes]
rs7661895	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7664396	0.93[AFR][1000 genomes];0.83[AMR][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:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102207600-102226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:102212600-102227200	Weak transcription	Primary T cells from cord blood	blood
3	chr4:102212800-102227200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr4:102212800-102228000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:102214800-102227200	Weak transcription	Gastric	stomach
6	chr4:102214800-102227200	Weak transcription	Psoas Muscle	Psoas
7	chr4:102215000-102227200	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:102215000-102227400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:102215000-102232600	Weak transcription	Pancreas	Pancrea
10	chr4:102215400-102236600	Weak transcription	Primary B cells from cord blood	blood
11	chr4:102216200-102227400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:102219200-102227400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:102221200-102226400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:102221600-102227000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:102221800-102226400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:102221800-102227400	Weak transcription	Small Intestine	intestine
17	chr4:102222000-102232800	Weak transcription	Lung	lung
18	chr4:102222200-102226400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:102222200-102228000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:102222400-102227400	Weak transcription	Adipose Nuclei	Adipose
21	chr4:102224000-102226600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:102224200-102226400	Weak transcription	Brain Angular Gyrus	brain
23	chr4:102225000-102226600	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr4:102225400-102227800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr4:102225400-102228000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:102225400-102228600	Enhancers	Brain Hippocampus Middle	brain
27	chr4:102225400-102228600	Enhancers	Brain Substantia Nigra	brain
28	chr4:102225400-102228800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr4:102225600-102228600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr4:102225600-102229200	Enhancers	Brain Anterior Caudate	brain
31	chr4:102225800-102227600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:102225800-102228200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:102225800-102229800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:102226000-102226400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr4:102226000-102226400	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr4:102226000-102226600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:102226000-102226600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr4:102226000-102226600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:102226000-102226600	Enhancers	Hela-S3	cervix
40	chr4:102226000-102227000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:102226000-102227000	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr4:102226000-102227200	Enhancers	GM12878-XiMat	blood
43	chr4:102226000-102227200	Enhancers	HMEC	breast
44	chr4:102226000-102227400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr4:102226000-102227600	Enhancers	Osteobl	bone
46	chr4:102226000-102228400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:102226000-102228400	Enhancers	NH-A	brain
48	chr4:102226000-102228600	Enhancers	H1 Cell Line	embryonic stem cell
49	chr4:102226000-102228800	Enhancers	A549	lung
50	chr4:102226000-102229200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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