Variant report

Variant	rs2172699
Chromosome Location	chr1:220925144-220925145
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	CEBPB	chr1:220925020-220925308	HepG2	liver:	n/a	chr1:220925172-220925183

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220923442..220925865-chr7:104652802..104654696,2	MCF-7	breast:

Variant related genes	Relation type
MARC2	TF binding region
ENSG00000239569	Chromatin interaction
ENSG00000005483	Chromatin interaction
ENSG00000228393	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17008595	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs17008643	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs2088044	0.85[EUR][1000 genomes]
rs2101771	0.85[EUR][1000 genomes]
rs2172700	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279636	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs2279637	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs58055537	0.81[EUR][1000 genomes]
rs6673650	0.81[EUR][1000 genomes]
rs72472365	0.87[EUR][1000 genomes]
rs72472382	0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922400-220932200	Weak transcription	HSMMtube	muscle
2	chr1:220922600-220925200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr1:220922600-220925200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:220922600-220925400	Weak transcription	Gastric	stomach
5	chr1:220922600-220927000	Weak transcription	Small Intestine	intestine
6	chr1:220922600-220928800	Weak transcription	Brain Substantia Nigra	brain
7	chr1:220922600-220929400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:220922600-220929400	Weak transcription	Esophagus	oesophagus
9	chr1:220922600-220931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:220922600-220943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:220922600-220946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:220922800-220925200	Enhancers	Stomach Mucosa	stomach
13	chr1:220922800-220925400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:220922800-220926000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:220922800-220929000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:220923000-220925200	Flanking Active TSS	Fetal Intestine Large	intestine
19	chr1:220923200-220925200	Enhancers	Colonic Mucosa	Colon
20	chr1:220923200-220925600	Enhancers	HepG2	liver
21	chr1:220923200-220926600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr1:220923200-220927200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:220923200-220927400	Enhancers	Pancreas	Pancrea
24	chr1:220923200-220930400	Weak transcription	Spleen	Spleen
25	chr1:220923200-220948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:220923400-220927000	Enhancers	Right Ventricle	heart
27	chr1:220923600-220926200	Enhancers	Psoas Muscle	Psoas
28	chr1:220923800-220925200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:220923800-220925200	Enhancers	Colon Smooth Muscle	Colon
30	chr1:220923800-220925600	Enhancers	Fetal Muscle Leg	muscle
31	chr1:220923800-220925800	Enhancers	Ovary	ovary
32	chr1:220923800-220928200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:220923800-220928200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:220923800-220928200	Weak transcription	Placenta	Placenta
35	chr1:220923800-220928400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:220924000-220925200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:220924000-220925200	Enhancers	Brain Cingulate Gyrus	brain
38	chr1:220924000-220925200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:220924000-220926000	Flanking Active TSS	Liver	Liver
40	chr1:220924000-220926000	Enhancers	Right Atrium	heart
41	chr1:220924000-220927200	Weak transcription	NHLF	lung
42	chr1:220924000-220927400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:220924000-220927600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr1:220924000-220928400	Weak transcription	Aorta	Aorta
45	chr1:220924000-220928600	Weak transcription	A549	lung
46	chr1:220924200-220925200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr1:220924200-220925200	Enhancers	Rectal Smooth Muscle	rectum
48	chr1:220924200-220925400	Enhancers	Fetal Brain Female	brain
49	chr1:220924200-220925400	Enhancers	Fetal Kidney	kidney
50	chr1:220924200-220925600	Enhancers	Fetal Brain Male	brain

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