Variant report

Variant	rs3858733
Chromosome Location	chr12:48237967-48237968
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48166574..48170045-chr12:48235326..48238478,3	MCF-7	breast:
2	chr12:48165936..48168416-chr12:48237403..48239336,2	K562	blood:
3	chr12:48221149..48222677-chr12:48237311..48239973,2	MCF-7	breast:
4	chr12:48236429..48238132-chr12:48243492..48246461,2	MCF-7	breast:
5	chr12:48236974..48239138-chr12:48244307..48246946,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000211584	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11574099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11574103	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574114	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs11574119	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11574139	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2853563	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs55748765	0.90[EUR][1000 genomes]
rs58789572	0.90[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3858733	PTH2R	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48223600-48238600	Weak transcription	Right Atrium	heart
2	chr12:48223600-48239800	Weak transcription	Gastric	stomach
3	chr12:48224200-48238400	Weak transcription	NHDF-Ad	bronchial
4	chr12:48224600-48238000	Weak transcription	Esophagus	oesophagus
5	chr12:48227200-48261200	Weak transcription	HSMM	muscle
6	chr12:48229800-48240200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:48231400-48261400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:48231800-48239000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:48232200-48253000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:48232400-48238200	Weak transcription	Aorta	Aorta
11	chr12:48232400-48263800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:48232400-48276600	Weak transcription	Pancreas	Pancrea
13	chr12:48232800-48238200	Weak transcription	Fetal Heart	heart
14	chr12:48233000-48275200	Weak transcription	Hela-S3	cervix
15	chr12:48233400-48238400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:48233800-48242600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:48233800-48242800	Weak transcription	K562	blood
18	chr12:48234600-48252400	Weak transcription	Stomach Mucosa	stomach
19	chr12:48235400-48238000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:48235800-48238800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:48235800-48239200	Weak transcription	Osteobl	bone
22	chr12:48236000-48239000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:48236200-48238000	Weak transcription	Ovary	ovary
24	chr12:48236200-48238200	Weak transcription	Fetal Lung	lung
25	chr12:48236200-48238200	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:48236200-48238400	Weak transcription	NHLF	lung
27	chr12:48236400-48252000	Strong transcription	Fetal Intestine Small	intestine
28	chr12:48236600-48238400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
29	chr12:48236600-48238400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
30	chr12:48236600-48243400	Strong transcription	HSMMtube	muscle
31	chr12:48236600-48259400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:48236800-48238000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:48236800-48238000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:48237000-48238000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:48237000-48238400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr12:48237000-48238600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:48237000-48239000	Bivalent Enhancer	Placenta	Placenta
38	chr12:48237000-48239200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:48237000-48239200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:48237000-48239200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:48237000-48241200	Strong transcription	Colonic Mucosa	Colon
42	chr12:48237000-48241200	Strong transcription	HMEC	breast
43	chr12:48237000-48242600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:48237000-48246800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr12:48237000-48252200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr12:48237000-48253200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:48237000-48259000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:48237000-48261800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr12:48237200-48238400	Strong transcription	Lung	lung
50	chr12:48237200-48238600	Strong transcription	NHEK	skin

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