Variant report

Variant	rs10036376
Chromosome Location	chr5:80548231-80548232
allele	C/T
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	CTCF	chr5:80548140-80548290	HepG2	liver:	n/a	n/a

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
CKMT2	TF binding region
ENSG00000131730	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10041063	0.85[CEU][hapmap]
rs10071174	0.84[EUR][1000 genomes]
rs10073527	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10074794	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10078279	0.82[CEU][hapmap]
rs10514215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10514216	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1055383	0.80[CEU][hapmap]
rs11950033	0.85[CEU][hapmap]
rs12516414	0.95[CEU][hapmap]
rs13155580	0.90[CEU][hapmap];0.82[CHB][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13170098	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13184427	1.00[JPT][hapmap]
rs1566432	0.82[CEU][hapmap]
rs16876403	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs16878572	1.00[JPT][hapmap]
rs17294956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270823	0.85[CEU][hapmap]
rs2270824	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs2270825	1.00[JPT][hapmap]
rs2277037	0.86[CEU][hapmap]
rs28819671	0.84[EUR][1000 genomes]
rs2897390	0.85[CEU][hapmap]
rs4703827	0.81[CEU][hapmap]
rs4703828	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs4704707	0.82[CEU][hapmap]
rs4704709	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4704710	0.85[CEU][hapmap]
rs4704717	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs545	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6859306	1.00[JPT][hapmap]
rs6872183	0.84[EUR][1000 genomes]
rs6893467	0.85[CEU][hapmap]
rs6899067	1.00[JPT][hapmap]
rs7448717	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs750728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7720009	0.82[CEU][hapmap]
rs7725743	1.00[JPT][hapmap]
rs976741	1.00[JPT][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10036376	CTC-281B15.1	cis	Thyroid	GTEx
rs10036376	CTC-281B15.1	cis	lung	GTEx
rs10036376	CTC-281B15.1	cis	Artery Aorta	GTEx
rs10036376	CTD-2248H3.1	cis	lung	GTEx
rs10036376	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs10036376	CTC-281B15.1	cis	Stomach	GTEx
rs10036376	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
2	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:80530800-80556400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr5:80531200-80551200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:80531200-80556400	Weak transcription	Thymus	Thymus
6	chr5:80531200-80564200	Weak transcription	HepG2	liver
7	chr5:80531800-80555800	Weak transcription	Fetal Lung	lung
8	chr5:80532000-80548400	Weak transcription	Lung	lung
9	chr5:80532200-80548400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:80532200-80551000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:80532200-80556800	Weak transcription	Dnd41	blood
12	chr5:80536200-80548600	Weak transcription	Fetal Intestine Small	intestine
13	chr5:80538400-80551400	Weak transcription	GM12878-XiMat	blood
14	chr5:80539000-80555200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:80539200-80548400	Weak transcription	Gastric	stomach
16	chr5:80541400-80549200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:80541800-80550600	Weak transcription	Fetal Intestine Large	intestine
18	chr5:80541800-80564400	Weak transcription	A549	lung
19	chr5:80542200-80557000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:80542400-80548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:80542800-80548400	Weak transcription	Esophagus	oesophagus
22	chr5:80542800-80548800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:80543000-80548400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:80543000-80554200	Weak transcription	Pancreas	Pancrea
25	chr5:80543600-80549000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:80543800-80565600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:80544000-80549200	Weak transcription	NHEK	skin
28	chr5:80544000-80549400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:80544000-80557000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr5:80544000-80564200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:80544000-80564400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:80544200-80549200	Weak transcription	HMEC	breast
33	chr5:80544200-80549400	Weak transcription	HSMM	muscle
34	chr5:80544200-80549800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:80544200-80550800	Weak transcription	Osteobl	bone
36	chr5:80544200-80551000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:80544200-80551200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:80544200-80561400	Weak transcription	NHLF	lung
39	chr5:80544200-80564600	Weak transcription	HSMMtube	muscle
40	chr5:80544400-80548400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:80544400-80550600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr5:80544400-80551400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr5:80545200-80550800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:80545200-80554400	Weak transcription	Ovary	ovary
45	chr5:80545200-80555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr5:80545400-80565200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr5:80545600-80549000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:80545800-80564800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:80546000-80548400	Enhancers	Fetal Heart	heart
50	chr5:80546200-80551200	Strong transcription	Fetal Stomach	stomach

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