Variant report

Variant	rs7720009
Chromosome Location	chr5:80541595-80541596
allele	A/G
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	chr5:80541550-80541631	K562	blood:	n/a	n/a
2	POLR2A	chr5:80541040-80542120	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80533844..80536662-chr5:80539256..80543290,4	K562	blood:
2	chr5:80540741..80543266-chr5:80561744..80563838,2	K562	blood:

Variant related genes	Relation type
ENSG00000248794	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs10036376	0.82[CEU][hapmap]
rs10038684	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053706	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055063	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10056565	0.83[ASN][1000 genomes]
rs10063615	0.83[ASN][1000 genomes]
rs10066296	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474656	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514213	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514215	0.85[CEU][hapmap]
rs1055383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942945	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13362314	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.87[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];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294956	0.85[CEU][hapmap]
rs2270823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406556	0.83[ASN][1000 genomes]
rs28464111	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897389	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2897390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703827	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704708	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704715	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704717	0.81[CEU][hapmap]
rs4704720	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545	0.81[CEU][hapmap]
rs59132806	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60488995	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60904680	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61244991	0.92[AMR][1000 genomes];0.90[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];0.89[AMR][1000 genomes];0.94[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];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130869	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7381116	0.84[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]
rs7728465	0.95[AMR][1000 genomes];0.90[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv2763877	chr5:80535750-80545341	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7720009	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs7720009	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs7720009	CTC-281B15.1	cis	Stomach	GTEx
rs7720009	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs7720009	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs7720009	CTC-281B15.1	cis	lung	GTEx
rs7720009	CTD-2248H3.1	cis	Thyroid	GTEx
rs7720009	CKMT2	cis	normal skin	skin_eQTL
rs7720009	CTC-281B15.1	cis	Thyroid	GTEx
rs7720009	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs7720009	CTC-281B15.1	cis	Artery Tibial	GTEx
rs7720009	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs7720009	CTC-281B15.1	cis	Artery Aorta	GTEx
rs7720009	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx
rs7720009	CTD-2248H3.1	cis	lung	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
3	chr5:80529400-80543400	Weak transcription	NHLF	lung
4	chr5:80529400-80544200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:80529600-80542800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:80529600-80545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:80530000-80546400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:80530200-80541600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:80530200-80544000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:80530600-80542800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:80530600-80543000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:80530600-80543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:80530600-80544000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:80530800-80556400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:80531200-80542400	Weak transcription	Primary T cells from cord blood	blood
17	chr5:80531200-80551200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:80531200-80556400	Weak transcription	Thymus	Thymus
19	chr5:80531200-80564200	Weak transcription	HepG2	liver
20	chr5:80531600-80542800	Weak transcription	Brain Germinal Matrix	brain
21	chr5:80531800-80543400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:80531800-80555800	Weak transcription	Fetal Lung	lung
23	chr5:80532000-80541600	Weak transcription	Fetal Brain Female	brain
24	chr5:80532000-80542600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:80532000-80548400	Weak transcription	Lung	lung
26	chr5:80532200-80548400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:80532200-80551000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr5:80532200-80556800	Weak transcription	Dnd41	blood
29	chr5:80532400-80541800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:80532600-80545200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:80534800-80542400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:80536000-80542000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:80536200-80542200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:80536200-80547800	Weak transcription	Spleen	Spleen
35	chr5:80536200-80548600	Weak transcription	Fetal Intestine Small	intestine
36	chr5:80537800-80545400	Genic enhancers	Left Ventricle	heart
37	chr5:80538000-80542000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:80538400-80542400	Genic enhancers	Fetal Muscle Leg	muscle
39	chr5:80538400-80542800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:80538400-80545000	Enhancers	Brain Cingulate Gyrus	brain
41	chr5:80538400-80551400	Weak transcription	GM12878-XiMat	blood
42	chr5:80538800-80542200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr5:80538800-80544800	Enhancers	Brain Hippocampus Middle	brain
44	chr5:80539000-80542400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:80539000-80555200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:80539200-80545200	Enhancers	Brain Substantia Nigra	brain
47	chr5:80539200-80548400	Weak transcription	Gastric	stomach
48	chr5:80539400-80543800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr5:80539600-80542600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:80539800-80542000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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