Variant report

Variant	rs12672488
Chromosome Location	chr7:102424959-102424960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10464611	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11974748	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4489255	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56356294	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73406218	0.82[ASN][1000 genomes]
rs7800387	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9641299	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9691949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv1828190	chr7:101966669-102439077	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv1025363	chr7:102072448-102471485	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1031471	chr7:102238120-102429404	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
6	nsv469620	chr7:102296392-102454063	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv482714	chr7:102296392-102454063	Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	esv2761100	chr7:102335787-102481978	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv470382	chr7:102375663-102538515	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv970564	chr7:102397635-102440049	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12672488	ZNF117	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102390000-102434400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:102390200-102432000	Weak transcription	Left Ventricle	heart
3	chr7:102390800-102448800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr7:102391000-102435400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr7:102391600-102448600	Weak transcription	Adipose Nuclei	Adipose
6	chr7:102404400-102432000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr7:102406000-102428600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr7:102410600-102430800	Weak transcription	HepG2	liver
9	chr7:102416400-102467600	Weak transcription	Brain Anterior Caudate	brain
10	chr7:102417000-102428400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:102417800-102431800	Weak transcription	A549	lung
12	chr7:102418800-102430600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr7:102419600-102454200	Weak transcription	Osteobl	bone
14	chr7:102419600-102456000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr7:102419800-102430200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:102419800-102454000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:102420400-102448600	Weak transcription	K562	blood
18	chr7:102420600-102435200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr7:102420800-102449000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr7:102421600-102425000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:102421600-102432800	Weak transcription	Ovary	ovary
22	chr7:102421600-102449000	Weak transcription	Liver	Liver
23	chr7:102421600-102452000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr7:102421600-102475600	Weak transcription	Fetal Thymus	thymus
25	chr7:102421800-102429600	Weak transcription	Fetal Brain Female	brain
26	chr7:102421800-102432000	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:102422000-102426600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:102422000-102431000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr7:102422000-102431400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:102422000-102431600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:102422000-102432000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr7:102422000-102435200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:102422000-102448800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:102422000-102474800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr7:102422000-102476000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr7:102422200-102432000	Weak transcription	Fetal Intestine Small	intestine
37	chr7:102422200-102432400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:102422200-102432600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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