Variant report

Variant	rs9293841
Chromosome Location	chr5:80543426-80543427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80543196..80546159-chr5:80550500..80552357,3	K562	blood:
2	chr5:80543196..80545536-chr5:80550500..80552357,2	K562	blood:

Variant related genes	Relation type
ENSG00000131730	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10038684	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041063	0.95[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];1.00[ASN][1000 genomes]
rs10053706	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055063	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10056565	0.83[ASN][1000 genomes]
rs10063615	0.83[ASN][1000 genomes]
rs10066296	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078279	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474656	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514215	0.81[CEU][hapmap]
rs1055383	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942945	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950033	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13362314	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566432	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]
rs17294418	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294956	0.81[CEU][hapmap]
rs2270823	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]
rs2406556	0.83[ASN][1000 genomes]
rs28464111	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650401	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897389	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2897390	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704707	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704708	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704710	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704712	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704715	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704720	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59132806	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60488995	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60904680	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61244991	0.95[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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6867884	0.83[ASN][1000 genomes]
rs6885028	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6893467	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130869	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7381116	0.87[AMR][1000 genomes]
rs7448717	0.88[CEU][hapmap]
rs750728	0.81[CEU][hapmap]
rs7709071	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7709149	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7720009	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728465	0.89[AFR][1000 genomes];0.97[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]

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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9293841	CTC-281B15.1	cis	Thyroid	GTEx
rs9293841	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs9293841	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs9293841	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs9293841	CTD-2248H3.1	cis	lung	GTEx
rs9293841	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs9293841	CTC-281B15.1	cis	Artery Aorta	GTEx
rs9293841	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx
rs9293841	CTD-2248H3.1	cis	Thyroid	GTEx
rs9293841	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs9293841	CTC-281B15.1	cis	Stomach	GTEx
rs9293841	CTC-281B15.1	cis	lung	GTEx
rs9293841	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs9293841	CTC-281B15.1	cis	Artery Tibial	GTEx
rs9293841	CTD-2248H3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs9293841	CKMT2	cis	normal skin	skin_eQTL

Chromatin state (count:95 , 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	chr5:80529400-80544200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:80529600-80545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:80530000-80546400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr5:80530200-80544000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:80530600-80543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:80530600-80544000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:80530800-80556400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:80531200-80551200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:80531200-80556400	Weak transcription	Thymus	Thymus
13	chr5:80531200-80564200	Weak transcription	HepG2	liver
14	chr5:80531800-80555800	Weak transcription	Fetal Lung	lung
15	chr5:80532000-80548400	Weak transcription	Lung	lung
16	chr5:80532200-80548400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:80532200-80551000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:80532200-80556800	Weak transcription	Dnd41	blood
19	chr5:80532600-80545200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:80536200-80547800	Weak transcription	Spleen	Spleen
21	chr5:80536200-80548600	Weak transcription	Fetal Intestine Small	intestine
22	chr5:80537800-80545400	Genic enhancers	Left Ventricle	heart
23	chr5:80538400-80545000	Enhancers	Brain Cingulate Gyrus	brain
24	chr5:80538400-80551400	Weak transcription	GM12878-XiMat	blood
25	chr5:80538800-80544800	Enhancers	Brain Hippocampus Middle	brain
26	chr5:80539000-80555200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr5:80539200-80545200	Enhancers	Brain Substantia Nigra	brain
28	chr5:80539200-80548400	Weak transcription	Gastric	stomach
29	chr5:80539400-80543800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr5:80540000-80544200	Enhancers	HSMMtube	muscle
31	chr5:80540200-80545400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr5:80540400-80544200	Enhancers	Stomach Mucosa	stomach
33	chr5:80540400-80544600	Enhancers	Brain Angular Gyrus	brain
34	chr5:80540800-80543800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:80540800-80544000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr5:80540800-80545400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr5:80541000-80543600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:80541000-80544800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:80541200-80544200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr5:80541200-80544200	Enhancers	HMEC	breast
41	chr5:80541200-80544400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:80541200-80544400	Enhancers	Brain Anterior Caudate	brain
43	chr5:80541400-80544600	Enhancers	Ovary	ovary
44	chr5:80541400-80549200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:80541600-80544400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:80541800-80544400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:80541800-80544600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:80541800-80550600	Weak transcription	Fetal Intestine Large	intestine
49	chr5:80541800-80564400	Weak transcription	A549	lung
50	chr5:80542000-80544200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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