Variant report

Variant	rs11172339
Chromosome Location	chr12:58184903-58184904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58135167..58137327-chr12:58184215..58186290,2	MCF-7	breast:
2	chr12:58183737..58188144-chr12:58191635..58196176,5	MCF-7	breast:
3	chr12:58184028..58186758-chr12:58191680..58194366,3	MCF-7	breast:
4	chr12:58179045..58181481-chr12:58182237..58185060,2	K562	blood:
5	chr12:58175481..58178584-chr12:58184682..58189368,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135439	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000123297	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11172336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11172340	0.80[AFR][1000 genomes]
rs11172348	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11555555	0.83[AMR][1000 genomes]
rs11829917	0.83[AMR][1000 genomes]
rs12297574	0.83[AMR][1000 genomes]
rs12297635	0.83[AMR][1000 genomes]
rs12297639	1.00[AMR][1000 genomes]
rs12321371	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1389302	1.00[AMR][1000 genomes]
rs8176348	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58177200-58189800	Weak transcription	Small Intestine	intestine
2	chr12:58177200-58197200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:58177400-58190000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:58177400-58192800	Weak transcription	Stomach Mucosa	stomach
5	chr12:58177400-58200400	Weak transcription	Fetal Heart	heart
6	chr12:58177400-58216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:58177600-58186400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:58177800-58187400	Strong transcription	Osteobl	bone
9	chr12:58177800-58188400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:58177800-58189600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:58177800-58191200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:58177800-58192200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:58177800-58198400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr12:58177800-58198400	Strong transcription	Fetal Muscle Leg	muscle
15	chr12:58177800-58199000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:58178000-58188600	Strong transcription	Fetal Lung	lung
17	chr12:58178000-58193200	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:58178000-58194200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:58178000-58197200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr12:58178000-58197600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:58178000-58198200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:58178000-58198200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:58178000-58198200	Strong transcription	Fetal Thymus	thymus
24	chr12:58178200-58197000	Strong transcription	Fetal Intestine Large	intestine
25	chr12:58178200-58197200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:58178200-58198200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr12:58178400-58191000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:58178400-58194000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:58178600-58187200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:58178600-58187400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:58178600-58187600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:58178600-58191400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:58178600-58207600	Strong transcription	Liver	Liver
34	chr12:58179000-58187400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:58179000-58187400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:58179000-58187400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:58179000-58188600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:58179000-58191400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr12:58179000-58191400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr12:58179000-58192000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr12:58179000-58192200	Strong transcription	Adipose Nuclei	Adipose
42	chr12:58179000-58193200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:58179000-58196800	Strong transcription	Thymus	Thymus
44	chr12:58179000-58197600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:58179000-58198200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:58179200-58186800	Strong transcription	Hela-S3	cervix
47	chr12:58179200-58187400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:58179200-58199000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:58179400-58187600	Strong transcription	A549	lung
50	chr12:58179400-58197400	Strong transcription	Duodenum Mucosa	Duodenum

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