Variant report

Variant	rs12516414
Chromosome Location	chr5:80593392-80593393
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	chr5:80592174..80595605-chr5:80595635..80599173,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247572	Chromatin interaction
ENSG00000131732	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10036376	0.95[CEU][hapmap]
rs10041063	0.81[CEU][hapmap]
rs10041138	0.84[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10052929	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs10055018	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10071174	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10073527	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10074794	0.84[EUR][1000 genomes]
rs10514215	0.95[CEU][hapmap]
rs10514216	0.90[EUR][1000 genomes]
rs11950033	0.81[CEU][hapmap]
rs11960275	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12514420	0.84[ASN][1000 genomes]
rs12652649	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12657721	0.81[JPT][hapmap]
rs12659947	0.91[JPT][hapmap]
rs13155580	0.95[CEU][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs13172928	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1566433	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs16876403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16878586	0.90[JPT][hapmap]
rs17294956	0.95[CEU][hapmap]
rs2270823	0.81[CEU][hapmap]
rs2270824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2277037	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291942	0.90[JPT][hapmap]
rs2406557	0.84[ASN][1000 genomes]
rs28819671	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2897390	0.81[CEU][hapmap]
rs4502795	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs4703828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4703832	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4703833	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4704709	0.83[EUR][1000 genomes]
rs4704710	0.81[CEU][hapmap]
rs4704714	0.85[CHB][hapmap]
rs4704716	0.91[JPT][hapmap]
rs4704717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs57086010	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57266451	0.81[ASN][1000 genomes]
rs60434474	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6863732	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs6868743	0.82[ASN][1000 genomes]
rs6872183	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6889795	0.81[ASN][1000 genomes]
rs6893467	0.81[CEU][hapmap]
rs6896441	0.81[ASN][1000 genomes]
rs7448717	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs750728	0.95[CEU][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	nsv819322	chr5:80591077-80593838	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12516414	CTC-281B15.1	cis	Thyroid	GTEx
rs12516414	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs12516414	CTC-281B15.1	cis	lung	GTEx
rs12516414	CTD-2248H3.1	cis	lung	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80572000-80595200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:80578800-80595200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:80581600-80595800	Weak transcription	Small Intestine	intestine
4	chr5:80584200-80595000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:80584400-80595000	Weak transcription	NH-A	brain
6	chr5:80586400-80595000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:80586400-80595000	Weak transcription	Hela-S3	cervix
8	chr5:80586800-80595200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:80587000-80595000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr5:80587000-80595000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:80588000-80595000	Weak transcription	Osteobl	bone
12	chr5:80588000-80595200	Weak transcription	A549	lung
13	chr5:80588200-80594600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr5:80588200-80594600	Weak transcription	Ovary	ovary
15	chr5:80588200-80595000	Weak transcription	NHLF	lung
16	chr5:80588200-80595200	Weak transcription	Right Atrium	heart
17	chr5:80588200-80596400	Weak transcription	Right Ventricle	heart
18	chr5:80588400-80593800	Weak transcription	HSMMtube	muscle
19	chr5:80588400-80595000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:80588400-80595200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:80588400-80595200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr5:80588400-80595200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:80588400-80595200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:80588400-80595800	Weak transcription	Left Ventricle	heart
25	chr5:80588400-80596400	Weak transcription	Psoas Muscle	Psoas
26	chr5:80588600-80596200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr5:80589400-80595200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:80589600-80595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:80589600-80595000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:80589600-80595000	Weak transcription	Brain Substantia Nigra	brain
31	chr5:80589600-80595200	Weak transcription	Brain Hippocampus Middle	brain
32	chr5:80589600-80595800	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:80589800-80595000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:80589800-80595200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr5:80589800-80595200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr5:80589800-80596000	Weak transcription	Fetal Intestine Large	intestine
37	chr5:80590000-80596000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:80590200-80595000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:80590200-80595200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:80590400-80595000	Weak transcription	Fetal Intestine Small	intestine
41	chr5:80590800-80594600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr5:80590800-80595200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr5:80590800-80595200	Weak transcription	HUVEC	blood vessel
44	chr5:80590800-80595800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:80591000-80593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:80591000-80594400	Weak transcription	Dnd41	blood
47	chr5:80591000-80594600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:80591000-80595000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:80591000-80595000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:80591000-80595000	Weak transcription	Fetal Lung	lung

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