Variant report

Variant	rs72679149
Chromosome Location	chr8:105599971-105599972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr8:105599933-105602287	K562	blood:	n/a	chr8:105600627-105600637 chr8:105601356-105601365
2	CHD1	chr8:105597872-105601900	GM12878	blood:	n/a	chr8:105601730-105601740
3	ARID3A	chr8:105599810-105600452	K562	blood:	n/a	n/a
4	TBL1XR1	chr8:105599620-105600603	K562	blood:	n/a	n/a
5	POLR2A	chr8:105596596-105602930	K562	blood:	n/a	n/a
6	TBP	chr8:105597820-105600273	GM12878	blood:	n/a	n/a
7	TEAD4	chr8:105599631-105600014	K562	blood:	n/a	n/a
8	MAZ	chr8:105599837-105602298	IMR90	lung:	n/a	chr8:105600627-105600637 chr8:105601356-105601365
9	CUX1	chr8:105599399-105600275	K562	blood:	n/a	n/a
10	POLR2A	chr8:105599711-105600032	GM12878	blood:	n/a	n/a
11	RCOR1	chr8:105599778-105602289	K562	blood:	n/a	n/a
12	POLR2A	chr8:105597878-105602244	GM12878	blood:	n/a	n/a
13	GATA3	chr8:105599963-105600274	SH-SY5Y	brain:	n/a	n/a
14	MXI1	chr8:105599894-105602519	IMR90	lung:	n/a	n/a
15	EP300	chr8:105599671-105599996	GM12878	blood:	n/a	chr8:105599740-105599750
16	MXI1	chr8:105598816-105602682	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:105599361..105601982-chr8:105602248..105604776,3	MCF-7	breast:
2	chr8:105587608..105589528-chr8:105597267..105600152,2	K562	blood:

Variant related genes	Relation type
ENSG00000253350	TF binding region
ENSG00000253350	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12541194	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12543329	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12543736	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12544422	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12546843	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12550349	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12680920	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12681417	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4461873	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4474003	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4609171	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510142	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66479713	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67341229	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67403507	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6988526	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72679139	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73295140	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7823668	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016087	chr8:105228670-105934368	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1026754	chr8:105382508-106030916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv539709	chr8:105382508-106030916	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv831417	chr8:105455814-105625608	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv508522	chr8:105532034-105614403	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2422460	chr8:105573376-105746329	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72679149	LRP12	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105584200-105600000	Weak transcription	Aorta	Aorta
2	chr8:105597600-105600000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr8:105598000-105600000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:105598000-105600000	Enhancers	Fetal Heart	heart
5	chr8:105598200-105600000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr8:105598200-105600000	Enhancers	Fetal Intestine Small	intestine
7	chr8:105598600-105602400	Active TSS	GM12878-XiMat	blood
8	chr8:105598800-105600000	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr8:105598800-105600600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr8:105598800-105602000	Active TSS	Brain Anterior Caudate	brain
11	chr8:105598800-105602000	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr8:105599000-105600000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:105599000-105600000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr8:105599000-105600200	Enhancers	Fetal Stomach	stomach
15	chr8:105599000-105602000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr8:105599200-105600000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
17	chr8:105599200-105600000	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr8:105599200-105600200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr8:105599200-105600200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr8:105599200-105602000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr8:105599200-105602400	Active TSS	Right Atrium	heart
22	chr8:105599200-105602400	Active TSS	Right Ventricle	heart
23	chr8:105599400-105600000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr8:105599400-105600000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr8:105599400-105600000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr8:105599400-105600000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr8:105599400-105600000	Enhancers	Fetal Intestine Large	intestine
28	chr8:105599400-105600000	Flanking Active TSS	Thymus	Thymus
29	chr8:105599400-105600000	Enhancers	Hela-S3	cervix
30	chr8:105599400-105600200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr8:105599400-105600200	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr8:105599400-105600200	Enhancers	Ovary	ovary
33	chr8:105599400-105600400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr8:105599400-105600600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr8:105599400-105600600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr8:105599400-105601000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr8:105599400-105602200	Active TSS	Left Ventricle	heart
38	chr8:105599600-105600000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr8:105599600-105600000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr8:105599600-105600000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
41	chr8:105599600-105600000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr8:105599600-105600000	Flanking Active TSS	Fetal Brain Male	brain
43	chr8:105599600-105600000	Flanking Active TSS	Fetal Lung	lung
44	chr8:105599600-105600000	Enhancers	HUVEC	blood vessel
45	chr8:105599600-105600000	Transcr. at gene 5' and 3'	K562	blood
46	chr8:105599600-105600000	Flanking Active TSS	NH-A	brain
47	chr8:105599600-105600000	Flanking Active TSS	NHDF-Ad	bronchial
48	chr8:105599600-105600000	Flanking Active TSS	NHEK	skin
49	chr8:105599600-105600200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
50	chr8:105599600-105600200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

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