Variant report

Variant	rs4566538
Chromosome Location	chr3:69258567-69258568
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69249207..69251218-chr3:69257048..69259660,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114541	Chromatin interaction

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

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

rs_ID	r²[population]
rs10865647	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11128120	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs11709719	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12631145	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12636686	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13088684	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34233715	0.87[EUR][1000 genomes]
rs4290807	0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4521234	1.00[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4635709	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[EUR][1000 genomes]
rs4855364	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs5028095	0.98[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6771291	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7433337	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7620845	0.82[ASN][1000 genomes]
rs9809129	0.81[JPT][hapmap]
rs9811034	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs9848667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9863613	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9873171	0.88[ASN][1000 genomes]
rs9873461	0.86[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	esv3398378	chr3:69240573-69271936	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69232000-69275600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:69242400-69281600	Weak transcription	Brain Germinal Matrix	brain
3	chr3:69242600-69268800	Weak transcription	Spleen	Spleen
4	chr3:69244000-69264800	Weak transcription	Fetal Brain Female	brain
5	chr3:69244200-69261800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:69246200-69266800	Weak transcription	HSMM	muscle
7	chr3:69249000-69263000	Weak transcription	Lung	lung
8	chr3:69250000-69261600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:69250000-69263000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:69250000-69269200	Weak transcription	Thymus	Thymus
11	chr3:69250000-69272400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:69250000-69281600	Weak transcription	Esophagus	oesophagus
13	chr3:69250200-69262000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:69250200-69262800	Weak transcription	Fetal Stomach	stomach
15	chr3:69250200-69263200	Weak transcription	Dnd41	blood
16	chr3:69250200-69268800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:69250200-69268800	Weak transcription	Ovary	ovary
18	chr3:69250200-69286000	Weak transcription	Colonic Mucosa	Colon
19	chr3:69250400-69260200	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:69250400-69264800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:69250400-69268400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:69250400-69280000	Weak transcription	Fetal Kidney	kidney
23	chr3:69253000-69266400	Weak transcription	Small Intestine	intestine
24	chr3:69253000-69297600	Weak transcription	Gastric	stomach
25	chr3:69253400-69259800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:69253400-69260600	Weak transcription	Fetal Intestine Small	intestine
27	chr3:69253400-69277400	Weak transcription	Left Ventricle	heart
28	chr3:69253600-69258600	Weak transcription	Hela-S3	cervix
29	chr3:69253600-69260400	Weak transcription	Stomach Mucosa	stomach
30	chr3:69253600-69260800	Weak transcription	Brain Anterior Caudate	brain
31	chr3:69253600-69263400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:69253600-69266600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:69253600-69267600	Weak transcription	Placenta	Placenta
34	chr3:69254000-69258600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:69254000-69260400	Weak transcription	Fetal Intestine Large	intestine
36	chr3:69254000-69260800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:69254000-69260800	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:69254000-69260800	Weak transcription	Brain Substantia Nigra	brain
39	chr3:69254000-69280800	Weak transcription	Pancreas	Pancrea
40	chr3:69254000-69286000	Weak transcription	Right Ventricle	heart
41	chr3:69254200-69261800	Weak transcription	Brain Angular Gyrus	brain
42	chr3:69254200-69261800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:69254200-69263600	Weak transcription	HSMMtube	muscle
44	chr3:69254600-69261200	Weak transcription	NHEK	skin
45	chr3:69254600-69262800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:69254600-69299000	Weak transcription	Fetal Brain Male	brain
47	chr3:69255000-69258800	Weak transcription	Fetal Heart	heart
48	chr3:69255600-69260400	Strong transcription	HUVEC	blood vessel
49	chr3:69255800-69259000	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr3:69256000-69260800	Weak transcription	Monocytes-CD14+_RO01746	blood

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