Variant report

Variant	rs1566432
Chromosome Location	chr5:80606814-80606815
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:80597031..80598832-chr5:80606167..80608882,2	K562	blood:
2	chr5:80599729..80604075-chr5:80605851..80609625,4	K562	blood:
3	chr5:80602575..80605016-chr5:80605616..80608114,3	K562	blood:
4	chr5:80605059..80607485-chr5:80614379..80616095,2	MCF-7	breast:
5	chr5:80595989..80598646-chr5:80605465..80607779,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131732	Chromatin interaction
ENSG00000247572	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10036376	0.82[CEU][hapmap]
rs10038684	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053706	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055063	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10056565	0.83[ASN][1000 genomes]
rs10063615	0.83[ASN][1000 genomes]
rs10066296	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474656	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514213	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514215	0.85[CEU][hapmap]
rs1055383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942945	0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13362314	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16876403	0.81[CEU][hapmap]
rs17294418	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294956	0.85[CEU][hapmap]
rs2270823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406556	0.83[ASN][1000 genomes]
rs28464111	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650401	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897389	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2897390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703827	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704708	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704712	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704715	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704717	0.81[CEU][hapmap]
rs4704720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545	0.81[CEU][hapmap]
rs59132806	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60488995	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60904680	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61244991	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365865	0.83[ASN][1000 genomes]
rs68077638	0.83[ASN][1000 genomes]
rs6866499	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6867884	0.83[ASN][1000 genomes]
rs6885028	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6893467	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130869	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7381116	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7448717	0.88[CEU][hapmap]
rs750728	0.85[CEU][hapmap]
rs7709071	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7709149	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7720009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728465	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7734902	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs921928	1.00[CHB][hapmap]
rs9293841	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1566432	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs1566432	CTD-2248H3.1	cis	lung	GTEx
rs1566432	CTC-281B15.1	cis	Thyroid	GTEx
rs1566432	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs1566432	CTC-281B15.1	cis	Stomach	GTEx
rs1566432	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs1566432	CKMT2	cis	normal skin	skin_eQTL
rs1566432	CTD-2248H3.1	cis	Thyroid	GTEx
rs1566432	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs1566432	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs1566432	CTC-281B15.1	cis	Artery Aorta	GTEx
rs1566432	CTC-281B15.1	cis	lung	GTEx
rs1566432	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx
rs1566432	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs1566432	CTD-2248H3.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80598200-80612400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:80598400-80611200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:80598600-80607000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:80598600-80607600	Weak transcription	Fetal Kidney	kidney
5	chr5:80598600-80608200	Weak transcription	Fetal Stomach	stomach
6	chr5:80598600-80608800	Weak transcription	Brain Germinal Matrix	brain
7	chr5:80598600-80609600	Weak transcription	Gastric	stomach
8	chr5:80598600-80610000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:80598600-80611200	Weak transcription	Brain Anterior Caudate	brain
10	chr5:80598600-80611200	Weak transcription	Fetal Brain Male	brain
11	chr5:80598600-80611200	Weak transcription	Small Intestine	intestine
12	chr5:80598600-80611200	Weak transcription	Stomach Mucosa	stomach
13	chr5:80598600-80611800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:80598800-80611000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:80598800-80611200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:80599200-80610000	Weak transcription	Pancreas	Pancrea
17	chr5:80599200-80612200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:80599400-80610400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:80599600-80609200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:80599600-80610600	Weak transcription	Fetal Heart	heart
21	chr5:80599600-80611200	Weak transcription	Brain Substantia Nigra	brain
22	chr5:80599800-80607000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:80599800-80608400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:80599800-80611400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:80601000-80607600	Weak transcription	GM12878-XiMat	blood
26	chr5:80601400-80611000	Weak transcription	Hela-S3	cervix
27	chr5:80601400-80612400	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:80601400-80612400	Weak transcription	Thymus	Thymus
29	chr5:80601600-80608200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:80601600-80611000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:80601600-80611200	Weak transcription	Colonic Mucosa	Colon
32	chr5:80601600-80611200	Weak transcription	Spleen	Spleen
33	chr5:80601600-80611600	Weak transcription	Esophagus	oesophagus
34	chr5:80601800-80607600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:80601800-80610000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:80602000-80609800	Weak transcription	K562	blood
37	chr5:80604000-80609800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:80604200-80610000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:80604200-80610000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:80604200-80611200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr5:80604200-80611400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:80604200-80611600	Strong transcription	Primary T cells from cord blood	blood
43	chr5:80604400-80607600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:80604400-80608400	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:80604400-80608400	Strong transcription	NHEK	skin
46	chr5:80604400-80608600	Strong transcription	Fetal Intestine Large	intestine
47	chr5:80604400-80608600	Strong transcription	Psoas Muscle	Psoas
48	chr5:80604400-80608800	Strong transcription	Fetal Muscle Leg	muscle
49	chr5:80604400-80609200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:80604400-80609800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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