Variant report

Variant	rs4925615
Chromosome Location	chr1:247465244-247465245
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247464530..247467054-chr1:247494594..247498451,4	K562	blood:
2	chr1:247457284..247461464-chr1:247462178..247466705,7	K562	blood:
3	chr1:247464828..247467490-chr1:247494042..247496164,2	MCF-7	breast:
4	chr1:247463122..247466119-chr1:247473298..247475329,2	K562	blood:
5	chr1:247461556..247465350-chr1:247467126..247471967,7	K562	blood:

Variant related genes	Relation type
ENSG00000162714	Chromatin interaction
ENSG00000202079	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10754542	0.95[ASN][1000 genomes]
rs10754544	0.81[CEU][hapmap]
rs10924985	0.92[ASN][1000 genomes]
rs10924989	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11578583	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1192830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1192831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1192832	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12035515	0.86[ASN][1000 genomes]
rs1204493	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1341173	0.81[ASN][1000 genomes]
rs1616299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1771929	0.83[ASN][1000 genomes]
rs1771943	0.94[ASN][1000 genomes]
rs1771948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1778544	0.98[ASN][1000 genomes]
rs1778546	0.97[ASN][1000 genomes]
rs1778549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2153631	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2799540	0.83[ASN][1000 genomes]
rs3850824	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4320815	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4925532	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4925533	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4925534	0.82[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4925621	0.83[ASN][1000 genomes]
rs56037169	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56399534	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674425	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6692645	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs74163745	0.83[ASN][1000 genomes]
rs7418221	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7528202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7540329	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7552292	0.93[ASN][1000 genomes]
rs875883	0.99[ASN][1000 genomes]
rs9426180	0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs9426181	0.98[ASN][1000 genomes]
rs9426182	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9426233	0.94[ASN][1000 genomes]
rs9725334	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4925615	EDIL3	trans	lymphoblastoid	RTeQTL
rs4925615	ZNF496	cis	temporal cortex	BrainEAC
rs4925615	ZNF496	cis	Nerve Tibial	GTEx
rs4925615	ZNF496	cis	brain	BrainEAC
rs4925615	ZNF496	cis	frontal cortex	BrainEAC

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
2	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
3	chr1:247456600-247471400	Weak transcription	Fetal Heart	heart
4	chr1:247457800-247466000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:247458000-247466800	Weak transcription	HSMMtube	muscle
6	chr1:247459800-247485800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:247460400-247493400	Strong transcription	Fetal Muscle Leg	muscle
8	chr1:247460800-247471600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:247460800-247474200	Strong transcription	Brain Germinal Matrix	brain
10	chr1:247460800-247474800	Strong transcription	Brain Cingulate Gyrus	brain
11	chr1:247460800-247476200	Weak transcription	HMEC	breast
12	chr1:247460800-247479800	Strong transcription	Fetal Brain Female	brain
13	chr1:247460800-247481000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:247460800-247491800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:247460800-247493400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:247461000-247468600	Strong transcription	Right Ventricle	heart
17	chr1:247461000-247469000	Strong transcription	Brain Anterior Caudate	brain
18	chr1:247461000-247475400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:247461000-247485400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:247461200-247465800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:247461200-247466000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:247461200-247473600	Weak transcription	HUVEC	blood vessel
23	chr1:247461200-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:247461200-247488200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:247461400-247471600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:247461400-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:247461400-247493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:247461600-247475200	Strong transcription	Aorta	Aorta
29	chr1:247461600-247481000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:247461800-247474200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr1:247462000-247466200	Strong transcription	Ovary	ovary
32	chr1:247462000-247466200	Strong transcription	Thymus	Thymus
33	chr1:247462000-247466600	Strong transcription	Brain Hippocampus Middle	brain
34	chr1:247462000-247468600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:247462000-247468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:247462000-247473800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:247462000-247473800	Strong transcription	Primary T cells from cord blood	blood
38	chr1:247462000-247474000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:247462000-247474000	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr1:247462200-247473800	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:247462200-247473800	Strong transcription	K562	blood
42	chr1:247462200-247480000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:247462400-247466400	Strong transcription	Gastric	stomach
44	chr1:247462400-247467200	Strong transcription	Adipose Nuclei	Adipose
45	chr1:247462400-247467600	Strong transcription	Spleen	Spleen
46	chr1:247462400-247468800	Strong transcription	Liver	Liver
47	chr1:247462400-247469000	Strong transcription	Brain Angular Gyrus	brain
48	chr1:247462400-247471000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:247462400-247473800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:247462400-247474000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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