Variant report

Variant	rs12485244
Chromosome Location	chr22:29427200-29427201
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29194663..29197354-chr22:29426484..29429608,3	K562	blood:
2	chr11:116658585..116659254-chr22:29427045..29427582,2	HCT-116	colon:
3	chr22:29193926..29196590-chr22:29426887..29431178,4	K562	blood:
4	chr22:29275977..29281461-chr22:29425203..29430435,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000109917	Chromatin interaction
ENSG00000183579	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12484832	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17440734	0.96[ASN][1000 genomes]
rs1977047	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2064084	0.95[ASN][1000 genomes]
rs2103544	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2347789	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2347790	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28541979	0.86[EUR][1000 genomes]
rs4140643	0.81[ASN][1000 genomes]
rs4333023	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4404379	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4594553	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4616575	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4820794	0.86[EUR][1000 genomes]
rs4823002	0.80[ASN][1000 genomes]
rs5997430	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997431	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997434	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997435	0.87[EUR][1000 genomes]
rs6005955	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005956	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6005958	0.97[ASN][1000 genomes]
rs6005959	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005964	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005965	0.86[EUR][1000 genomes]
rs6005967	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713834	0.88[EUR][1000 genomes]
rs727892	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7284304	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7287517	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs738246	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8137254	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8142591	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs874915	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs874916	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9608719	0.82[EUR][1000 genomes]
rs9608721	0.85[EUR][1000 genomes]
rs9613771	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613776	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9613777	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9613784	0.86[EUR][1000 genomes]
rs9613785	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs964589	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:155 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29420600-29427800	Weak transcription	Brain Substantia Nigra	brain
2	chr22:29425200-29427400	Weak transcription	Gastric	stomach
3	chr22:29425800-29427600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:29425800-29428800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:29425800-29429000	Enhancers	Fetal Heart	heart
6	chr22:29426000-29427200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr22:29426000-29427200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr22:29426000-29427200	Active TSS	Rectal Smooth Muscle	rectum
9	chr22:29426000-29427600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr22:29426000-29427600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
11	chr22:29426000-29428600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr22:29426000-29428800	Bivalent Enhancer	Fetal Thymus	thymus
13	chr22:29426000-29429000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr22:29426000-29429000	Enhancers	Stomach Mucosa	stomach
15	chr22:29426200-29427200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr22:29426200-29427200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr22:29426200-29427200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr22:29426200-29427200	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr22:29426200-29427200	Active TSS	Aorta	Aorta
20	chr22:29426200-29427200	Active TSS	Brain Hippocampus Middle	brain
21	chr22:29426200-29427200	Active TSS	Pancreas	Pancrea
22	chr22:29426200-29427200	Active TSS	Psoas Muscle	Psoas
23	chr22:29426200-29427200	Active TSS	Right Atrium	heart
24	chr22:29426200-29427200	Weak transcription	Small Intestine	intestine
25	chr22:29426200-29427400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr22:29426200-29427400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr22:29426200-29427400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr22:29426200-29428200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr22:29426400-29427200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr22:29426400-29427200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr22:29426400-29427200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr22:29426400-29427200	Active TSS	Brain Anterior Caudate	brain
33	chr22:29426400-29427200	Active TSS	Colon Smooth Muscle	Colon
34	chr22:29426400-29427200	Active TSS	Duodenum Mucosa	Duodenum
35	chr22:29426400-29427200	Active TSS	Esophagus	oesophagus
36	chr22:29426400-29427200	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr22:29426400-29427200	Active TSS	Left Ventricle	heart
38	chr22:29426400-29427200	Active TSS	Placenta Amnion	Placenta Amnion
39	chr22:29426400-29427200	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr22:29426400-29427200	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr22:29426400-29427200	Active TSS	Hela-S3	cervix
42	chr22:29426400-29427200	Active TSS	HSMMtube	muscle
43	chr22:29426400-29428000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr22:29426400-29430000	Enhancers	Lung	lung
45	chr22:29426600-29427200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr22:29426600-29427200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr22:29426600-29427200	Active TSS	Liver	Liver
48	chr22:29426600-29427200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
49	chr22:29426600-29427200	Active TSS	Fetal Lung	lung
50	chr22:29426600-29427200	Active TSS	A549	lung

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