Variant report

Variant	rs55667372
Chromosome Location	chr4:102264111-102264112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:102264062-102264213	MCF-7	breast:	n/a	n/a
2	FOXA1	chr4:102263913-102264206	T-47D	breast:	n/a	chr4:102264056-102264071
3	POLR2A	chr4:102264063-102264439	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102263328..102265199-chr4:102265515..102267436,2	K562	blood:
2	chr4:102048414..102050219-chr4:102262763..102264265,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254531	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1011849	0.92[AFR][1000 genomes]
rs1372243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1372244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1441431	0.98[AFR][1000 genomes]
rs1561722	0.97[AFR][1000 genomes]
rs17031168	0.92[AFR][1000 genomes]
rs17031172	0.98[AFR][1000 genomes]
rs17031175	0.98[AFR][1000 genomes]
rs17031176	0.98[AFR][1000 genomes]
rs17031180	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17031182	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3789755	0.82[AFR][1000 genomes]
rs3974659	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4488940	0.88[AFR][1000 genomes]
rs4504259	0.88[AFR][1000 genomes]
rs4637408	0.92[AFR][1000 genomes]
rs58629361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59079781	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59224049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59763039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60438397	0.97[AFR][1000 genomes]
rs60984918	0.98[AFR][1000 genomes]
rs6532924	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6532925	0.98[AFR][1000 genomes]
rs6532926	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6810812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6812094	0.98[AFR][1000 genomes]
rs6817805	0.81[AFR][1000 genomes]
rs6827528	0.88[AFR][1000 genomes]
rs6828025	0.88[AFR][1000 genomes]
rs6830390	0.88[AFR][1000 genomes]
rs6831471	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6831824	0.81[AFR][1000 genomes]
rs6832020	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6834721	0.92[AFR][1000 genomes]
rs6837858	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6842191	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6844844	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6846554	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6852282	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835923	0.87[AFR][1000 genomes]
rs73835924	0.92[AFR][1000 genomes]
rs73835931	0.92[AFR][1000 genomes]
rs73835933	0.92[AFR][1000 genomes]
rs73835934	0.98[AFR][1000 genomes]
rs73835935	0.98[AFR][1000 genomes]
rs73835936	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835937	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835938	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73835939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835943	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835944	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7661895	0.98[AFR][1000 genomes]
rs7664396	0.98[AFR][1000 genomes]
rs7671524	0.84[AFR][1000 genomes];0.91[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:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102249600-102266400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:102250200-102265200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:102250400-102265800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:102250600-102266000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:102251200-102265800	Weak transcription	Brain Hippocampus Middle	brain
6	chr4:102252000-102265800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:102252200-102266000	Weak transcription	Fetal Lung	lung
8	chr4:102252800-102266400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:102254000-102266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:102255200-102266400	Weak transcription	Gastric	stomach
11	chr4:102255400-102266600	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:102256400-102265800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr4:102256600-102264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:102256600-102266000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:102256800-102265800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:102256800-102266200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:102257000-102264200	Weak transcription	Ovary	ovary
18	chr4:102257000-102266400	Weak transcription	Left Ventricle	heart
19	chr4:102257000-102266400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:102257000-102266400	Weak transcription	Right Ventricle	heart
21	chr4:102257000-102266400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:102257600-102266600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:102258000-102266200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:102258200-102266400	Weak transcription	Spleen	Spleen
25	chr4:102258400-102266000	Weak transcription	HepG2	liver
26	chr4:102258600-102264800	Weak transcription	Dnd41	blood
27	chr4:102258800-102265800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:102258800-102265800	Weak transcription	Adipose Nuclei	Adipose
29	chr4:102258800-102266400	Weak transcription	HSMM	muscle
30	chr4:102259000-102264200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr4:102259000-102265800	Weak transcription	Brain Germinal Matrix	brain
32	chr4:102259000-102266400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:102259200-102264400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:102259200-102265000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:102259200-102266600	Weak transcription	Pancreas	Pancrea
36	chr4:102259400-102265600	Weak transcription	NH-A	brain
37	chr4:102259400-102265600	Weak transcription	NHLF	lung
38	chr4:102259400-102265800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:102259400-102266200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr4:102259600-102265600	Weak transcription	NHDF-Ad	bronchial
41	chr4:102259600-102265800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr4:102259600-102266000	Weak transcription	Osteobl	bone
43	chr4:102259800-102265800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:102260000-102265800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr4:102260200-102264200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:102260400-102265800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:102260400-102265800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr4:102260400-102266000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:102260400-102266200	Weak transcription	Right Atrium	heart
50	chr4:102260400-102266400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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