Variant report

Variant	rs2853563
Chromosome Location	chr12:48235738-48235739
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48166658..48168237-chr12:48233792..48236686,2	K562	blood:
2	chr12:48226837..48229758-chr12:48234295..48236180,2	K562	blood:
3	chr12:48166574..48170045-chr12:48235326..48238478,3	MCF-7	breast:
4	chr12:48176329..48178651-chr12:48234485..48237249,2	K562	blood:
5	chr12:48233637..48235954-chr12:48241553..48243456,2	K562	blood:
6	chr12:48230667..48234164-chr12:48234323..48236614,4	K562	blood:

Variant related genes	Relation type
ENSG00000211584	Chromatin interaction
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11574099	0.83[EUR][1000 genomes]
rs11574103	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11574114	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs11574119	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11574139	0.93[EUR][1000 genomes]
rs11574146	0.90[AFR][1000 genomes]
rs2525045	1.00[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs3858733	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs55748765	0.97[EUR][1000 genomes]
rs58789572	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
4	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48223400-48236800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr12:48223400-48237000	Weak transcription	Colonic Mucosa	Colon
3	chr12:48223600-48237000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:48223600-48238600	Weak transcription	Right Atrium	heart
5	chr12:48223600-48239800	Weak transcription	Gastric	stomach
6	chr12:48224200-48238400	Weak transcription	NHDF-Ad	bronchial
7	chr12:48224600-48238000	Weak transcription	Esophagus	oesophagus
8	chr12:48227200-48261200	Weak transcription	HSMM	muscle
9	chr12:48227600-48237400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:48229000-48237200	Weak transcription	Lung	lung
11	chr12:48229000-48237200	Weak transcription	Spleen	Spleen
12	chr12:48229800-48236600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:48229800-48237400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr12:48229800-48240200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:48230000-48236600	Weak transcription	HSMMtube	muscle
16	chr12:48230000-48237000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:48230000-48237600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:48230400-48235800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:48230600-48235800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:48231400-48236200	Enhancers	Fetal Muscle Leg	muscle
21	chr12:48231400-48261400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:48231600-48237000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:48231600-48237000	Weak transcription	HMEC	breast
24	chr12:48231800-48236000	Weak transcription	NHEK	skin
25	chr12:48231800-48237000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:48231800-48239000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:48232200-48253000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:48232400-48237400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:48232400-48238200	Weak transcription	Aorta	Aorta
30	chr12:48232400-48263800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:48232400-48276600	Weak transcription	Pancreas	Pancrea
32	chr12:48232800-48237000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:48232800-48238200	Weak transcription	Fetal Heart	heart
34	chr12:48233000-48235800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:48233000-48237000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:48233000-48275200	Weak transcription	Hela-S3	cervix
37	chr12:48233400-48237000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:48233400-48238400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:48233600-48235800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr12:48233600-48237800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:48233800-48235800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:48233800-48242600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:48233800-48242800	Weak transcription	K562	blood
44	chr12:48234200-48237400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:48234600-48236000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:48234600-48252400	Weak transcription	Stomach Mucosa	stomach
47	chr12:48234800-48236200	Enhancers	Ovary	ovary
48	chr12:48234800-48237000	Enhancers	Placenta	Placenta
49	chr12:48234800-48237000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr12:48235000-48236200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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