Variant report

Variant	rs17472416
Chromosome Location	chr15:77795932-77795933
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:77447640..77449355-chr15:77793706..77796059,2	MCF-7	breast:
2	chr15:77481285..77483374-chr15:77795738..77797524,2	MCF-7	breast:
3	chr15:77786574..77788334-chr15:77795705..77797965,2	MCF-7	breast:
4	chr15:77795830..77799057-chr15:77830706..77834217,3	MCF-7	breast:
5	chr15:77795040..77797177-chr15:77834449..77837320,2	MCF-7	breast:
6	chr15:77795420..77798597-chr15:77834386..77837370,5	MCF-7	breast:
7	chr15:77793912..77796870-chr15:77807695..77810216,2	MCF-7	breast:
8	chr15:77793877..77796515-chr15:77817397..77819668,3	MCF-7	breast:
9	chr15:77788815..77791032-chr15:77793939..77797001,3	MCF-7	breast:
10	chr15:77789779..77791418-chr15:77794224..77796698,3	MCF-7	breast:
11	chr15:77710223..77714353-chr15:77793653..77797346,4	MCF-7	breast:
12	chr15:77789312..77792548-chr15:77795862..77798378,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259362	Chromatin interaction
ENSG00000173517	Chromatin interaction
ENSG00000140382	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10519165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12898522	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901298	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905890	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906093	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12912739	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917211	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917347	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384857	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17386174	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17469938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949269	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864841	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34023254	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34137991	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34158220	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34197100	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34237392	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34344208	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34410684	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34607003	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34660075	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34664675	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34665451	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34690222	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34772392	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34858590	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34905779	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34918566	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35015654	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35277326	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35347401	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35383172	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35420345	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35450609	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35628983	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35775156	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35778082	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35834995	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35892909	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36103772	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4288963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4349115	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007266	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007269	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62007278	0.89[ASN][1000 genomes]
rs62007303	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007307	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007310	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007313	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007316	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007337	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007338	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007340	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62007343	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010561	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010567	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72742499	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031202	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats 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	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv570140	chr15:77787469-77851535	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17472416	SGK269	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77777600-77798600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:77786200-77800000	Weak transcription	Thymus	Thymus
3	chr15:77786400-77799600	Weak transcription	Primary B cells from cord blood	blood
4	chr15:77786400-77803800	Weak transcription	Primary T cells from cord blood	blood
5	chr15:77789800-77796400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:77789800-77798600	Weak transcription	Gastric	stomach
7	chr15:77789800-77799600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:77789800-77801000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:77790200-77799200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr15:77790600-77799200	Weak transcription	GM12878-XiMat	blood
11	chr15:77791000-77796000	Weak transcription	Liver	Liver
12	chr15:77791000-77797000	Weak transcription	Lung	lung
13	chr15:77791000-77797400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:77791000-77797400	Weak transcription	Pancreas	Pancrea
15	chr15:77791000-77797800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:77791000-77798600	Weak transcription	HSMM	muscle
17	chr15:77791000-77798800	Weak transcription	Fetal Intestine Large	intestine
18	chr15:77791200-77796200	Weak transcription	Esophagus	oesophagus
19	chr15:77791200-77796800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:77791200-77797000	Weak transcription	Fetal Intestine Small	intestine
21	chr15:77791600-77796000	Weak transcription	Spleen	Spleen
22	chr15:77791600-77797000	Weak transcription	Fetal Brain Female	brain
23	chr15:77791600-77798600	Weak transcription	Fetal Kidney	kidney
24	chr15:77791600-77798800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:77791600-77798800	Weak transcription	Osteobl	bone
26	chr15:77791600-77799000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:77791800-77796000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:77791800-77797000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:77791800-77798200	Weak transcription	Fetal Thymus	thymus
30	chr15:77792000-77796200	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:77792000-77796600	Weak transcription	Adipose Nuclei	Adipose
32	chr15:77792000-77796800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:77792000-77798800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:77792000-77799200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr15:77792200-77796000	Weak transcription	Fetal Lung	lung
36	chr15:77792200-77796200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:77792200-77796200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:77792200-77796400	Weak transcription	Fetal Stomach	stomach
39	chr15:77792200-77796600	Weak transcription	Fetal Heart	heart
40	chr15:77792200-77797000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:77792400-77797000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:77793800-77796000	Weak transcription	Right Ventricle	heart
43	chr15:77793800-77797200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:77793800-77797200	Weak transcription	Right Atrium	heart
45	chr15:77793800-77798000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:77793800-77798600	Weak transcription	NHDF-Ad	bronchial
47	chr15:77794000-77796600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:77794000-77797200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:77794000-77797400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:77794000-77798600	Weak transcription	NHLF	lung

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