Variant report

Variant	rs11172262
Chromosome Location	chr12:57990135-57990136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57980291..57988961-chr12:57988993..57992835,10	MCF-7	breast:
2	chr12:57989594..57991495-chr12:57993172..57994871,2	MCF-7	breast:
3	chr12:57983454..57989400-chr12:57989791..58002327,29	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166908	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10747780	0.82[ASN][1000 genomes]
rs1806652	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2619439	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34181394	0.84[EUR][1000 genomes]
rs60586224	0.86[EUR][1000 genomes]
rs71461330	0.87[EUR][1000 genomes]
rs7305391	0.88[EUR][1000 genomes]
rs7314872	0.89[EUR][1000 genomes]
rs7964896	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs812315	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8873	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
6	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv725	chr12:57966549-57993808	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11172262	ARHGEF25	cis	Nerve Tibial	GTEx
rs11172262	AC025165.8	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57985800-57998000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:57985800-57998400	Weak transcription	HSMMtube	muscle
3	chr12:57986000-57990400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:57986000-57992800	Weak transcription	Aorta	Aorta
5	chr12:57986200-57991800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:57986200-57992400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr12:57986200-57992600	Weak transcription	Ovary	ovary
8	chr12:57986200-57992800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:57986200-57992800	Weak transcription	Fetal Kidney	kidney
10	chr12:57986200-57992800	Weak transcription	Psoas Muscle	Psoas
11	chr12:57986200-57993400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:57986200-57993600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:57986200-57993800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:57986200-57994600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:57986200-57994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:57986200-57997200	Weak transcription	Fetal Lung	lung
17	chr12:57986200-57997400	Weak transcription	Right Atrium	heart
18	chr12:57986200-57997400	Weak transcription	NHDF-Ad	bronchial
19	chr12:57986400-57998000	Weak transcription	NHLF	lung
20	chr12:57986600-57990200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:57986600-57992800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:57986600-57992800	Weak transcription	Osteobl	bone
23	chr12:57986600-57993200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:57986600-57997600	Weak transcription	NH-A	brain
25	chr12:57986600-57998200	Weak transcription	HSMM	muscle
26	chr12:57986800-57992800	Weak transcription	Small Intestine	intestine
27	chr12:57987000-57997200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:57987200-57990400	Weak transcription	HepG2	liver
29	chr12:57987200-57992800	Weak transcription	Brain Germinal Matrix	brain
30	chr12:57987200-57992800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:57987200-57992800	Weak transcription	Right Ventricle	heart
32	chr12:57987200-57992800	Weak transcription	GM12878-XiMat	blood
33	chr12:57987200-57996600	Strong transcription	Stomach Smooth Muscle	stomach
34	chr12:57987200-57997200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:57987200-57998400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr12:57987400-57992400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:57987400-57994000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr12:57987400-57997400	Weak transcription	Fetal Brain Male	brain
39	chr12:57987600-57990400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:57987600-57990800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:57987600-57996200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr12:57987600-57996400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr12:57987600-57996400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr12:57987600-57996600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:57987600-57996600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr12:57987600-57996600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:57987600-57996800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:57987600-57996800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:57987600-57997000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:57987600-57997000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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