Variant report

Variant	rs17784472
Chromosome Location	chr6:131335052-131335053
allele	A/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	POLR2A	chr6:131334613-131335072	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr6:131334564-131335202	SK-N-MC	brain:	n/a	n/a
3	GATA2	chr6:131334638-131335266	HUVEC	blood vessel:	n/a	chr6:131334852-131334860

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs12525104	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525986	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13437326	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17178878	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17179123	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17180687	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17180867	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17784418	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17784896	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17785507	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1811949	0.89[ASN][1000 genomes]
rs1977576	0.95[ASN][1000 genomes]
rs2297853	0.89[ASN][1000 genomes]
rs28482889	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34899420	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4895901	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4895903	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895904	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895906	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895907	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895908	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895909	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897477	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4897478	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897483	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897485	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897486	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897487	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897489	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897491	1.00[ASN][1000 genomes]
rs55898152	1.00[ASN][1000 genomes]
rs56163502	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56173113	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56201801	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58503799	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62422362	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62422365	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62422380	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62423581	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62423597	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62423598	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6906059	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6916024	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921396	0.89[ASN][1000 genomes]
rs6922045	0.89[ASN][1000 genomes]
rs6928920	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931804	0.80[AMR][1000 genomes]
rs6935108	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741148	0.89[ASN][1000 genomes]
rs7755720	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7758016	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769678	0.89[ASN][1000 genomes]
rs7771543	0.89[ASN][1000 genomes]
rs9385568	0.89[ASN][1000 genomes]
rs9402303	0.89[ASN][1000 genomes]
rs9483206	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954211	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17784472	EPB41L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131329800-131336400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:131329800-131347400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:131330200-131335400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:131330400-131336400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:131332200-131345400	Weak transcription	Left Ventricle	heart
6	chr6:131332800-131339600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:131333400-131335400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:131333600-131339200	Weak transcription	Pancreas	Pancrea
9	chr6:131333800-131337400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:131334000-131337000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:131334000-131337400	Enhancers	Fetal Kidney	kidney
12	chr6:131334400-131335200	Active TSS	Ovary	ovary
13	chr6:131334400-131335400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr6:131334400-131335400	Enhancers	NH-A	brain
15	chr6:131334400-131335800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:131334400-131337200	Weak transcription	Small Intestine	intestine
17	chr6:131334400-131337400	Enhancers	HMEC	breast
18	chr6:131334600-131335200	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr6:131334600-131335200	Flanking Active TSS	Fetal Lung	lung
20	chr6:131334600-131335400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr6:131334600-131335400	Flanking Active TSS	HUVEC	blood vessel
22	chr6:131334600-131335600	Enhancers	Primary hematopoietic stem cells	blood
23	chr6:131334600-131335600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:131334600-131335800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:131334600-131336600	Enhancers	Dnd41	blood
26	chr6:131334600-131338000	Enhancers	Fetal Stomach	stomach
27	chr6:131334600-131338200	Enhancers	HepG2	liver
28	chr6:131334600-131338200	Enhancers	Osteobl	bone
29	chr6:131334600-131339000	Enhancers	Rectal Smooth Muscle	rectum
30	chr6:131334800-131335200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:131334800-131335200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:131334800-131335200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:131334800-131335200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:131334800-131335200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:131334800-131335200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr6:131334800-131335200	Flanking Active TSS	Aorta	Aorta
37	chr6:131334800-131335200	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr6:131334800-131335200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr6:131334800-131335200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr6:131334800-131335200	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr6:131334800-131335200	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr6:131334800-131335200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr6:131334800-131335200	Flanking Active TSS	NHDF-Ad	bronchial
44	chr6:131334800-131335200	Flanking Active TSS	NHLF	lung
45	chr6:131334800-131335400	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr6:131334800-131335800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:131334800-131335800	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr6:131334800-131336600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr6:131334800-131336600	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr6:131334800-131336800	Enhancers	HUES48 Cell Line	embryonic stem cell

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