Variant report

Variant	rs4760158
Chromosome Location	chr12:57988478-57988479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57983454..57989400-chr12:57989791..58002327,29	MCF-7	breast:
2	chr12:57926277..57928720-chr12:57987336..57989718,2	MCF-7	breast:
3	chr12:57983601..57985889-chr12:57986664..57989043,2	K562	blood:

Variant related genes	Relation type
ENSG00000166908	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000178498	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10747780	0.95[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs10747781	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11537654	0.89[JPT][hapmap]
rs1545783	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1806652	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs2306390	0.84[JPT][hapmap]
rs4760304	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs812315	0.86[CEU][hapmap];0.80[TSI][hapmap]

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
rs4760158	AC025165.8	cis	Nerve Tibial	GTEx
rs4760158	ARHGEF25	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	chr12:57986000-57989200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:57986000-57989400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:57986000-57989400	Weak transcription	Adipose Nuclei	Adipose
6	chr12:57986000-57989600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:57986000-57990400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:57986000-57992800	Weak transcription	Aorta	Aorta
9	chr12:57986200-57988800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:57986200-57988800	Weak transcription	Placenta	Placenta
11	chr12:57986200-57989000	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:57986200-57989000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:57986200-57989000	Weak transcription	Left Ventricle	heart
14	chr12:57986200-57989200	Weak transcription	Brain Substantia Nigra	brain
15	chr12:57986200-57989200	Weak transcription	Fetal Stomach	stomach
16	chr12:57986200-57989400	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:57986200-57989400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:57986200-57989600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:57986200-57989600	Weak transcription	Liver	Liver
20	chr12:57986200-57991800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:57986200-57992400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:57986200-57992600	Weak transcription	Ovary	ovary
23	chr12:57986200-57992800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:57986200-57992800	Weak transcription	Fetal Kidney	kidney
25	chr12:57986200-57992800	Weak transcription	Psoas Muscle	Psoas
26	chr12:57986200-57993400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:57986200-57993600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:57986200-57993800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:57986200-57994600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:57986200-57994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:57986200-57997200	Weak transcription	Fetal Lung	lung
32	chr12:57986200-57997400	Weak transcription	Right Atrium	heart
33	chr12:57986200-57997400	Weak transcription	NHDF-Ad	bronchial
34	chr12:57986400-57989000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:57986400-57989000	Weak transcription	Fetal Brain Female	brain
36	chr12:57986400-57989200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:57986400-57998000	Weak transcription	NHLF	lung
38	chr12:57986600-57988800	Weak transcription	Hela-S3	cervix
39	chr12:57986600-57989200	Weak transcription	Thymus	Thymus
40	chr12:57986600-57989400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:57986600-57989400	Weak transcription	Spleen	Spleen
42	chr12:57986600-57989600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:57986600-57989600	Weak transcription	Colonic Mucosa	Colon
44	chr12:57986600-57989600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:57986600-57990200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:57986600-57992800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:57986600-57992800	Weak transcription	Osteobl	bone
48	chr12:57986600-57993200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr12:57986600-57997600	Weak transcription	NH-A	brain
50	chr12:57986600-57998200	Weak transcription	HSMM	muscle

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