Variant report

Variant	rs5762449
Chromosome Location	chr22:28409162-28409163
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28312284..28315668-chr22:28406606..28409523,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235954	Chromatin interaction
ENSG00000180957	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11912165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2064360	1.00[CHB][hapmap]
rs2235574	0.80[EUR][1000 genomes]
rs2294969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28720063	0.82[ASN][1000 genomes]
rs56695231	0.97[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs5752658	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs5752679	1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5752687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752690	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs5762408	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs5762446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5762474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs5762478	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs5762492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs5762495	0.80[ASN][1000 genomes]
rs5762498	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs5762506	0.82[ASN][1000 genomes]
rs5762508	1.00[CEU][hapmap];1.00[CHB][hapmap]

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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 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	chr22:28381800-28412400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr22:28386200-28416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr22:28389200-28410000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr22:28389200-28413000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr22:28390000-28414600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr22:28390400-28416200	Weak transcription	Colonic Mucosa	Colon
7	chr22:28394800-28414000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr22:28395000-28416400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr22:28395200-28409200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:28395400-28409200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr22:28395600-28413000	Weak transcription	Pancreas	Pancrea
12	chr22:28396000-28422400	Weak transcription	Primary T cells from cord blood	blood
13	chr22:28397200-28409400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr22:28397200-28423000	Weak transcription	HepG2	liver
15	chr22:28397400-28412000	Weak transcription	Placenta	Placenta
16	chr22:28399400-28425800	Weak transcription	Liver	Liver
17	chr22:28400800-28410200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr22:28401600-28412000	Weak transcription	Thymus	Thymus
19	chr22:28401800-28410400	Weak transcription	Fetal Thymus	thymus
20	chr22:28402400-28409600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr22:28405200-28414000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr22:28405400-28412400	Weak transcription	Brain Hippocampus Middle	brain
23	chr22:28405400-28415000	Weak transcription	HSMM	muscle
24	chr22:28405400-28416200	Weak transcription	NHDF-Ad	bronchial
25	chr22:28405400-28416200	Weak transcription	NHLF	lung
26	chr22:28405400-28416400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr22:28405400-28416400	Weak transcription	Fetal Kidney	kidney
28	chr22:28405600-28412400	Weak transcription	Brain Anterior Caudate	brain
29	chr22:28405600-28414800	Weak transcription	HSMMtube	muscle
30	chr22:28405800-28409200	Weak transcription	Brain Substantia Nigra	brain
31	chr22:28405800-28409400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr22:28405800-28410000	Weak transcription	Fetal Brain Male	brain
33	chr22:28405800-28411400	Strong transcription	Fetal Intestine Small	intestine
34	chr22:28405800-28414000	Weak transcription	Psoas Muscle	Psoas
35	chr22:28405800-28416000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr22:28405800-28416200	Weak transcription	Left Ventricle	heart
37	chr22:28406200-28409800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr22:28406200-28410800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr22:28406200-28411200	Strong transcription	Fetal Stomach	stomach
40	chr22:28406600-28410600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr22:28406800-28411000	Strong transcription	Ovary	ovary
42	chr22:28406800-28411800	Weak transcription	Fetal Heart	heart
43	chr22:28407000-28409200	Weak transcription	Esophagus	oesophagus
44	chr22:28407400-28409800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr22:28407400-28410400	Strong transcription	Aorta	Aorta
46	chr22:28407600-28409800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr22:28407600-28410800	Strong transcription	Adipose Nuclei	Adipose
48	chr22:28407600-28411000	Strong transcription	Fetal Intestine Large	intestine
49	chr22:28407600-28411800	Strong transcription	Dnd41	blood
50	chr22:28407800-28409200	Strong transcription	Brain Germinal Matrix	brain

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