Variant report

Variant	rs2270823
Chromosome Location	chr5:80552871-80552872
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	chr5:80547726..80550284-chr5:80550387..80553255,3	K562	blood:
2	chr5:80546433..80550284-chr5:80550387..80553828,5	K562	blood:

Variant related genes	Relation type
ENSG00000131730	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs10036376	0.85[CEU][hapmap]
rs10038684	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053706	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055063	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10056565	0.83[ASN][1000 genomes]
rs10063615	0.83[ASN][1000 genomes]
rs10066296	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10073527	0.81[CEU][hapmap]
rs10078279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474656	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514213	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[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];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942945	0.93[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12516414	0.81[CEU][hapmap]
rs13362314	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566432	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]
rs16876403	0.81[CEU][hapmap]
rs17294418	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294956	0.85[CEU][hapmap]
rs2270824	0.81[CEU][hapmap]
rs2406556	0.83[ASN][1000 genomes]
rs28464111	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650401	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897389	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2897390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703827	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704708	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704712	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704715	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704717	0.81[CEU][hapmap]
rs4704720	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545	0.81[CEU][hapmap]
rs59132806	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60488995	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60904680	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61244991	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[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];0.89[AMR][1000 genomes];0.90[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];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130869	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7381116	0.89[AMR][1000 genomes]
rs7448717	0.94[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];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728465	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[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];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	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
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2270823	CTD-2248H3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2270823	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs2270823	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs2270823	CTD-2248H3.1	cis	lung	GTEx
rs2270823	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs2270823	CTC-281B15.1	cis	Stomach	GTEx
rs2270823	CKMT2	cis	normal skin	skin_eQTL
rs2270823	CTC-281B15.1	cis	lung	GTEx
rs2270823	CTC-281B15.1	cis	Artery Aorta	GTEx
rs2270823	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs2270823	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs2270823	CTC-281B15.1	cis	Thyroid	GTEx
rs2270823	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs2270823	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx
rs2270823	CTD-2248H3.1	cis	Thyroid	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
2	chr5:80530800-80556400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr5:80531200-80556400	Weak transcription	Thymus	Thymus
4	chr5:80531200-80564200	Weak transcription	HepG2	liver
5	chr5:80531800-80555800	Weak transcription	Fetal Lung	lung
6	chr5:80532200-80556800	Weak transcription	Dnd41	blood
7	chr5:80539000-80555200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:80541800-80564400	Weak transcription	A549	lung
9	chr5:80542200-80557000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:80543000-80554200	Weak transcription	Pancreas	Pancrea
11	chr5:80543800-80565600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:80544000-80557000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:80544000-80564200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:80544000-80564400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:80544200-80561400	Weak transcription	NHLF	lung
16	chr5:80544200-80564600	Weak transcription	HSMMtube	muscle
17	chr5:80545200-80554400	Weak transcription	Ovary	ovary
18	chr5:80545200-80555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:80545400-80565200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr5:80545800-80564800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:80546600-80556800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:80546600-80564600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:80547200-80553800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:80547600-80555600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:80547800-80555400	Strong transcription	Aorta	Aorta
26	chr5:80548200-80555600	Strong transcription	Fetal Muscle Leg	muscle
27	chr5:80548200-80557600	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:80548200-80559400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:80548400-80555600	Strong transcription	Right Ventricle	heart
30	chr5:80548800-80554200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:80548800-80554200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:80548800-80554600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:80548800-80559400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr5:80548800-80568000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr5:80549000-80554800	Weak transcription	Brain Angular Gyrus	brain
36	chr5:80549200-80561400	Weak transcription	Liver	Liver
37	chr5:80549200-80562000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:80549400-80554400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:80549400-80554400	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:80549400-80565800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:80549400-80565800	Weak transcription	Lung	lung
42	chr5:80550200-80553800	Weak transcription	HMEC	breast
43	chr5:80550200-80554400	Weak transcription	Primary T cells from cord blood	blood
44	chr5:80550200-80560400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:80550400-80553400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:80550400-80554000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:80550400-80554800	Weak transcription	Brain Substantia Nigra	brain
48	chr5:80550400-80563800	Weak transcription	NHEK	skin
49	chr5:80550400-80564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:80550800-80564000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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