Variant report

Variant	rs28450055
Chromosome Location	chr12:49856402-49856403
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	chr12:49849137..49852050-chr12:49855425..49857339,2	K562	blood:
2	chr12:49759519..49761735-chr12:49853453..49856491,3	K562	blood:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10160947	0.83[ASN][1000 genomes]
rs10161131	0.83[ASN][1000 genomes]
rs10506284	1.00[ASN][1000 genomes]
rs11168988	1.00[ASN][1000 genomes]
rs11169015	1.00[ASN][1000 genomes]
rs11169016	1.00[ASN][1000 genomes]
rs11169017	1.00[ASN][1000 genomes]
rs11169027	1.00[ASN][1000 genomes]
rs11611743	1.00[ASN][1000 genomes]
rs11834161	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299282	1.00[ASN][1000 genomes]
rs12301632	1.00[ASN][1000 genomes]
rs12302036	0.83[ASN][1000 genomes]
rs12306118	1.00[ASN][1000 genomes]
rs12306212	1.00[ASN][1000 genomes]
rs12306645	1.00[ASN][1000 genomes]
rs12310836	0.81[AMR][1000 genomes]
rs12314428	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12316170	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12318633	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12320284	1.00[ASN][1000 genomes]
rs12322319	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57108124	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57601151	1.00[ASN][1000 genomes]
rs59250459	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61340540	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580707	1.00[ASN][1000 genomes]
rs6580709	1.00[ASN][1000 genomes]
rs6580710	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580711	1.00[ASN][1000 genomes]
rs6580716	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132684	1.00[ASN][1000 genomes]
rs7139061	1.00[ASN][1000 genomes]
rs7294973	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7295162	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309997	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73295291	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73295300	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297209	1.00[ASN][1000 genomes]
rs73297210	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297243	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73301240	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7342365	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74089066	1.00[ASN][1000 genomes]
rs7955541	1.00[ASN][1000 genomes]
rs7961032	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7962951	1.00[ASN][1000 genomes]
rs7964718	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7969010	1.00[ASN][1000 genomes]
rs7969099	1.00[ASN][1000 genomes]
rs7976165	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
2	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:49823400-49857400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:49823400-49876000	Weak transcription	Osteobl	bone
4	chr12:49828000-49863400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:49839200-49876000	Weak transcription	Fetal Thymus	thymus
6	chr12:49840200-49900600	Weak transcription	Pancreas	Pancrea
7	chr12:49840600-49875800	Weak transcription	Hela-S3	cervix
8	chr12:49845800-49856800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr12:49846000-49879800	Weak transcription	Fetal Lung	lung
10	chr12:49846400-49878400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:49847000-49858200	Weak transcription	Fetal Brain Female	brain
12	chr12:49849400-49875800	Weak transcription	HepG2	liver
13	chr12:49849600-49869800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:49850000-49858800	Weak transcription	Fetal Kidney	kidney
15	chr12:49850400-49876000	Weak transcription	Fetal Intestine Large	intestine
16	chr12:49850400-49876000	Weak transcription	Small Intestine	intestine
17	chr12:49850400-49878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:49850400-49911000	Weak transcription	K562	blood
19	chr12:49850600-49876200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:49853200-49876000	Weak transcription	HSMMtube	muscle
21	chr12:49853200-49913400	Weak transcription	Thymus	Thymus
22	chr12:49854200-49856800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:49854400-49856800	Strong transcription	Dnd41	blood
24	chr12:49854400-49857000	Strong transcription	NH-A	brain
25	chr12:49854400-49878400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:49854600-49856800	Enhancers	Duodenum Mucosa	Duodenum
27	chr12:49854600-49858000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:49855000-49856800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:49855000-49856800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr12:49855000-49856800	Strong transcription	Brain Germinal Matrix	brain
31	chr12:49855000-49858200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:49855200-49857800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:49855200-49861400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:49855200-49872600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:49855400-49869800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:49855600-49870000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:49855800-49856800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:49855800-49856800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:49856000-49856600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:49856000-49856600	Strong transcription	Primary T cells from cord blood	blood
41	chr12:49856000-49856600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:49856000-49856600	Enhancers	Adipose Nuclei	Adipose
43	chr12:49856000-49856600	Enhancers	Liver	Liver
44	chr12:49856000-49856600	Enhancers	Brain Hippocampus Middle	brain
45	chr12:49856000-49856600	Enhancers	Brain Substantia Nigra	brain
46	chr12:49856000-49856600	Genic enhancers	Fetal Muscle Leg	muscle
47	chr12:49856000-49856600	Strong transcription	Ovary	ovary
48	chr12:49856000-49856800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:49856000-49856800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:49856000-49856800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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