Variant report

Variant	rs17303015
Chromosome Location	chr5:43194137-43194138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43191118..43192645-chr5:43192728..43194544,2	K562	blood:
2	chr5:43120206..43121723-chr5:43192557..43194191,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177453	Chromatin interaction
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10050724	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10512821	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10941609	1.00[CHB][hapmap];0.88[MEX][hapmap]
rs11745619	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746055	1.00[CHB][hapmap];0.88[MEX][hapmap]
rs11747314	0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs11748138	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11748652	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12110174	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514198	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514283	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12522830	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1845485	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2004946	1.00[ASN][1000 genomes]
rs35186274	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55714804	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55735646	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55740753	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55770582	1.00[ASN][1000 genomes]
rs55780226	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55967719	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56003146	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56081223	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6868031	1.00[ASN][1000 genomes]
rs6871615	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748871	0.80[AFR][1000 genomes]
rs72748894	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72750768	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72752504	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72752507	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72752511	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72752578	1.00[ASN][1000 genomes]
rs72752594	1.00[ASN][1000 genomes]
rs72752599	1.00[ASN][1000 genomes]
rs7730107	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17303015	C5orf39	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43191000-43194200	Active TSS	Brain Anterior Caudate	brain
2	chr5:43191200-43194200	Active TSS	NHDF-Ad	bronchial
3	chr5:43191200-43194400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr5:43191200-43194800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:43191600-43194600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:43191600-43194800	Active TSS	Brain Angular Gyrus	brain
7	chr5:43191800-43194200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr5:43191800-43195000	Active TSS	Brain Substantia Nigra	brain
9	chr5:43192000-43194200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr5:43192000-43194200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:43192000-43194200	Active TSS	Brain Hippocampus Middle	brain
12	chr5:43192000-43194200	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr5:43192000-43194600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:43192200-43194600	Active TSS	NHLF	lung
15	chr5:43192400-43194400	Flanking Active TSS	NH-A	brain
16	chr5:43192600-43194400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr5:43192600-43194400	Flanking Active TSS	GM12878-XiMat	blood
18	chr5:43192800-43194200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:43193000-43194200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:43193000-43194200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:43193000-43194200	Active TSS	Right Atrium	heart
22	chr5:43193000-43194200	Active TSS	Stomach Smooth Muscle	stomach
23	chr5:43193000-43194400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:43193000-43194600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr5:43193200-43194200	Weak transcription	Left Ventricle	heart
26	chr5:43193200-43194400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:43193200-43194400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:43193200-43194400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
29	chr5:43193200-43194400	Bivalent Enhancer	Fetal Intestine Large	intestine
30	chr5:43193200-43194400	Enhancers	Pancreas	Pancrea
31	chr5:43193200-43194400	Flanking Active TSS	Hela-S3	cervix
32	chr5:43193400-43194200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr5:43193400-43194200	Enhancers	Liver	Liver
34	chr5:43193400-43194200	Active TSS	Rectal Smooth Muscle	rectum
35	chr5:43193400-43194400	Bivalent Enhancer	Fetal Heart	heart
36	chr5:43193600-43194200	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr5:43193600-43194200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
38	chr5:43193600-43194200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr5:43193600-43194200	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr5:43193600-43194200	Flanking Active TSS	K562	blood
41	chr5:43193600-43194400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
42	chr5:43193600-43194400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
43	chr5:43193600-43194400	Active TSS	Colonic Mucosa	Colon
44	chr5:43193600-43194400	Bivalent Enhancer	Fetal Intestine Small	intestine
45	chr5:43193800-43194200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:43193800-43194200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:43193800-43194200	Enhancers	Fetal Brain Male	brain
48	chr5:43193800-43194200	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
49	chr5:43193800-43194200	Enhancers	Stomach Mucosa	stomach
50	chr5:43193800-43194200	Flanking Active TSS	A549	lung

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