Variant report

Variant	rs3753879
Chromosome Location	chr1:220934802-220934803
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:220934709..220937356-chr1:220938309..220941059,2	K562	blood:
2	chr1:220933592..220936563-chr1:220940646..220943203,2	MCF-7	breast:
3	chr1:220932351..220934813-chr1:220937381..220940360,2	K562	blood:
4	chr1:220932972..220935057-chr1:220960206..220962159,2	MCF-7	breast:
5	chr1:220921708..220923550-chr1:220934385..220936474,2	MCF-7	breast:
6	chr1:220926792..220928893-chr1:220934076..220936520,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11589296	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11809755	0.86[EUR][1000 genomes]
rs12407624	0.89[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1494373	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17008587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275575	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337163	0.90[EUR][1000 genomes]
rs337166	0.84[EUR][1000 genomes]
rs337167	0.84[EUR][1000 genomes]
rs337168	0.84[EUR][1000 genomes]
rs337174	0.84[EUR][1000 genomes]
rs337182	0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs337188	0.94[EUR][1000 genomes]
rs337192	0.90[EUR][1000 genomes]
rs3753878	0.86[EUR][1000 genomes]
rs41314538	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59423796	0.90[EUR][1000 genomes]
rs61830238	0.90[EUR][1000 genomes]
rs61830262	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6659246	0.87[EUR][1000 genomes]
rs774139	0.89[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][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	nsv523389	chr1:220926844-220956012	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922600-220943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:220922600-220946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:220923200-220948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:220924200-220936000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:220924600-220936800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:220924600-220944000	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:220924800-220945600	Weak transcription	Osteobl	bone
10	chr1:220925000-220946000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:220925000-220959400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:220925200-220942000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:220925200-220943400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:220925400-220950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:220925800-220938400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:220927800-220938600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:220929400-220940600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:220929600-220935800	Weak transcription	Esophagus	oesophagus
19	chr1:220929600-220943000	Weak transcription	Brain Germinal Matrix	brain
20	chr1:220929800-220940800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:220930000-220940600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:220930000-220942400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:220930000-220943400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:220930000-220946000	Weak transcription	Fetal Brain Female	brain
25	chr1:220930000-220950000	Weak transcription	Fetal Brain Male	brain
26	chr1:220930000-220950200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:220930000-220950400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:220930000-220959600	Weak transcription	Psoas Muscle	Psoas
29	chr1:220930200-220935200	Weak transcription	Placenta	Placenta
30	chr1:220930200-220935800	Weak transcription	Colonic Mucosa	Colon
31	chr1:220930200-220936200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:220930200-220937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:220930200-220940800	Weak transcription	NHLF	lung
34	chr1:220930200-220944000	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:220930200-220950000	Weak transcription	Brain Anterior Caudate	brain
36	chr1:220930400-220950000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:220930400-220959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:220930600-220950000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:220930800-220935200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:220930800-220946000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:220931000-220935800	Weak transcription	Spleen	Spleen
42	chr1:220931000-220946200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:220931200-220935200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:220931200-220935600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:220931200-220935800	Weak transcription	A549	lung
46	chr1:220931200-220940400	Weak transcription	Fetal Kidney	kidney
47	chr1:220931200-220942400	Weak transcription	Hela-S3	cervix
48	chr1:220931200-220946600	Weak transcription	HUVEC	blood vessel
49	chr1:220931200-220959000	Weak transcription	Brain Substantia Nigra	brain
50	chr1:220931400-220944400	Weak transcription	Muscle Satellite Cultured Cells	--

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