Variant report

Variant	rs17294956
Chromosome Location	chr5:80540556-80540557
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80533844..80536662-chr5:80539256..80543290,4	K562	blood:
2	chr5:80537672..80539759-chr5:80539987..80541535,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248794	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10036376	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]
rs10041063	0.85[CEU][hapmap]
rs10073527	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10074794	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10078279	0.87[CEU][hapmap]
rs10514213	0.81[CEU][hapmap]
rs10514215	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10514216	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1055383	0.84[CEU][hapmap]
rs11950033	0.85[CEU][hapmap]
rs11960275	0.81[EUR][1000 genomes]
rs12516414	0.95[CEU][hapmap]
rs13155580	0.89[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13170098	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13184427	1.00[JPT][hapmap]
rs1566432	0.85[CEU][hapmap]
rs16876403	0.95[CEU][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs16878572	1.00[JPT][hapmap]
rs17294418	0.81[CEU][hapmap]
rs2270823	0.85[CEU][hapmap]
rs2270824	0.95[CEU][hapmap];0.84[YRI][hapmap];0.85[EUR][1000 genomes]
rs2270825	1.00[JPT][hapmap]
rs2277037	0.86[CEU][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2897389	0.80[CEU][hapmap]
rs2897390	0.85[CEU][hapmap]
rs4703827	0.81[CEU][hapmap]
rs4703828	0.95[CEU][hapmap]
rs4704707	0.85[CEU][hapmap]
rs4704709	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4704710	0.85[CEU][hapmap]
rs4704717	0.95[CEU][hapmap];0.89[TSI][hapmap]
rs545	0.83[ASW][hapmap];0.95[CEU][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57086010	0.85[EUR][1000 genomes]
rs60434474	0.84[EUR][1000 genomes]
rs6859306	1.00[JPT][hapmap]
rs6893467	0.85[CEU][hapmap]
rs6899067	1.00[JPT][hapmap]
rs7448717	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs750728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7720009	0.85[CEU][hapmap]
rs7725743	1.00[JPT][hapmap]
rs9293841	0.81[CEU][hapmap]
rs976741	1.00[JPT][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17294956	CTC-281B15.1	cis	Artery Aorta	GTEx
rs17294956	CTC-281B15.1	cis	lung	GTEx
rs17294956	CTC-281B15.1	cis	Thyroid	GTEx
rs17294956	CTC-281B15.1	cis	Stomach	GTEx
rs17294956	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs17294956	CTD-2248H3.1	cis	lung	GTEx

Chromatin state (count:82 , 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	chr5:80529400-80540800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:80529400-80541000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:80529400-80543400	Weak transcription	NHLF	lung
6	chr5:80529400-80544200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:80529600-80541000	Weak transcription	Fetal Intestine Large	intestine
9	chr5:80529600-80542800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:80529600-80545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:80530000-80546400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:80530200-80541600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:80530200-80544000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:80530600-80542800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:80530600-80543000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:80530600-80543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:80530600-80544000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:80530800-80556400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:80531200-80542400	Weak transcription	Primary T cells from cord blood	blood
20	chr5:80531200-80551200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:80531200-80556400	Weak transcription	Thymus	Thymus
22	chr5:80531200-80564200	Weak transcription	HepG2	liver
23	chr5:80531600-80542800	Weak transcription	Brain Germinal Matrix	brain
24	chr5:80531800-80541000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:80531800-80543400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:80531800-80555800	Weak transcription	Fetal Lung	lung
27	chr5:80532000-80540800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:80532000-80541600	Weak transcription	Fetal Brain Female	brain
29	chr5:80532000-80542600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:80532000-80548400	Weak transcription	Lung	lung
31	chr5:80532200-80548400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:80532200-80551000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:80532200-80556800	Weak transcription	Dnd41	blood
34	chr5:80532400-80541800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:80532600-80545200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:80534800-80542400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:80535400-80541000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:80536000-80541200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:80536000-80541200	Enhancers	Fetal Heart	heart
40	chr5:80536000-80542000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:80536200-80540800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:80536200-80541000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr5:80536200-80541200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:80536200-80542200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:80536200-80547800	Weak transcription	Spleen	Spleen
46	chr5:80536200-80548600	Weak transcription	Fetal Intestine Small	intestine
47	chr5:80536400-80540600	Weak transcription	Fetal Stomach	stomach
48	chr5:80537200-80540800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:80537600-80540600	Enhancers	Psoas Muscle	Psoas
50	chr5:80537600-80541200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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