Variant report

Variant	rs1489108
Chromosome Location	chr12:48738781-48738782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48737402..48739098-chr12:48743829..48745442,2	MCF-7	breast:
2	chr12:48737714..48740514-chr12:48742056..48744740,4	K562	blood:
3	chr12:48738698..48740838-chr12:48743123..48744667,2	K562	blood:
4	chr12:48727374..48736715-chr12:48738720..48747602,13	K562	blood:

Variant related genes	Relation type
ENSG00000167528	Chromatin interaction
ENSG00000257735	Chromatin interaction
ENSG00000258273	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1061986	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1107654	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12828309	0.87[AMR][1000 genomes]
rs1387259	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1387260	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1552550	0.87[AMR][1000 genomes]
rs1601985	0.82[AMR][1000 genomes]
rs2054905	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2409003	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2409004	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2450994	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2468943	0.86[EUR][1000 genomes]
rs2634670	0.84[AMR][1000 genomes]
rs2634676	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2634678	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2634680	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2634681	0.91[EUR][1000 genomes]
rs2634682	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2634684	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2634686	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2634688	0.88[EUR][1000 genomes]
rs2634689	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2634691	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2634692	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2634693	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2634694	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2732441	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2732445	0.85[AMR][1000 genomes]
rs2732448	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2732453	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2732454	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2732457	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2732461	0.87[AMR][1000 genomes]
rs2732462	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2732466	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2732479	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2732481	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2732484	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2732486	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2732488	0.82[AMR][1000 genomes]
rs2956703	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2956710	0.89[AMR][1000 genomes]
rs923397	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv437752	chr12:48721832-48741219	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv1045159	chr12:48730024-48748940	Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1489108	H1FNT	cis	Muscle Skeletal	GTEx
rs1489108	H1FNT	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48729000-48739200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:48729200-48743400	Weak transcription	Stomach Mucosa	stomach
3	chr12:48731200-48743800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:48732400-48742600	Strong transcription	Left Ventricle	heart
5	chr12:48732600-48742600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:48733200-48742000	Strong transcription	Brain Hippocampus Middle	brain
7	chr12:48733200-48742200	Strong transcription	Fetal Thymus	thymus
8	chr12:48733400-48739600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:48733400-48741000	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr12:48733600-48742000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:48733600-48742200	Strong transcription	Primary B cells from cord blood	blood
12	chr12:48733600-48743800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:48733800-48742000	Strong transcription	Liver	Liver
14	chr12:48733800-48742200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:48733800-48742800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:48734000-48741800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:48734000-48741800	Strong transcription	Fetal Brain Female	brain
18	chr12:48734000-48742000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:48734000-48742200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr12:48734000-48742600	Strong transcription	Fetal Muscle Leg	muscle
21	chr12:48734200-48742000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr12:48734600-48739000	Weak transcription	A549	lung
23	chr12:48734600-48741800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:48734600-48742000	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr12:48734800-48741600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:48735000-48743000	Weak transcription	Fetal Heart	heart
27	chr12:48735200-48743600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:48735400-48742000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:48735400-48742000	Strong transcription	Stomach Smooth Muscle	stomach
30	chr12:48735400-48742200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:48735400-48742600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:48735400-48743200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:48735600-48741400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:48735600-48741800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:48735600-48742000	Strong transcription	Brain Germinal Matrix	brain
36	chr12:48735600-48742000	Strong transcription	Fetal Intestine Large	intestine
37	chr12:48735600-48742000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr12:48735800-48741600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:48735800-48741800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr12:48735800-48741800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:48735800-48741800	Strong transcription	Adipose Nuclei	Adipose
42	chr12:48735800-48742000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:48735800-48742200	Strong transcription	Brain Anterior Caudate	brain
44	chr12:48735800-48742400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:48736000-48741600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:48736000-48741600	Strong transcription	Brain Angular Gyrus	brain
47	chr12:48736000-48741800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:48736000-48741800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:48736000-48741800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr12:48736000-48741800	Strong transcription	Brain Substantia Nigra	brain

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