Variant report

Variant	rs17717859
Chromosome Location	chr15:40094564-40094565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr15:40094100-40094566	GM12878	blood:	n/a	n/a
2	CTCF	chr15:40094019-40094566	MCF-7	breast:	n/a	n/a
3	CTCF	chr15:40094048-40094568	MCF-7	breast:	n/a	n/a
4	SMC3	chr15:40093899-40094610	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr15:40093928-40094665	A549	lung:	n/a	n/a
6	RAD21	chr15:40094018-40094580	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr15:40094480-40094630	HMF	breast:	n/a	n/a
8	CTCF	chr15:40094090-40094601	HCT-116	colon:	n/a	n/a
9	CTCF	chr15:40093733-40094632	SK-N-SH	brain:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40093805..40094865-chr15:40166415..40167459,6	MCF-7	breast:
2	chr15:40075150..40077007-chr15:40093645..40095814,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259580	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10520141	1.00[CHB][hapmap]
rs10520143	1.00[CHB][hapmap]
rs10520146	1.00[CHB][hapmap]
rs10520147	1.00[CHB][hapmap]
rs10520148	1.00[CHB][hapmap]
rs10520151	0.80[CEU][hapmap]
rs1073675	1.00[CHB][hapmap]
rs12903306	0.80[CEU][hapmap]
rs12910355	1.00[JPT][hapmap]
rs16969487	1.00[CHB][hapmap]
rs16969491	1.00[CHB][hapmap]
rs16969547	1.00[CHB][hapmap]
rs16969663	1.00[CHB][hapmap]
rs16969664	1.00[CHB][hapmap]
rs16969666	1.00[CHB][hapmap]
rs16969672	1.00[CHB][hapmap]
rs16969679	1.00[CHB][hapmap]
rs16969680	1.00[CHB][hapmap]
rs16969688	1.00[CHB][hapmap]
rs17633210	1.00[CHB][hapmap]
rs17705806	1.00[CHB][hapmap]
rs17706083	1.00[CHB][hapmap]
rs17706179	1.00[CHB][hapmap]
rs1994380	1.00[CHB][hapmap]
rs2129457	1.00[CHB][hapmap]
rs2171311	0.80[CEU][hapmap]
rs2411316	1.00[CHB][hapmap]
rs2576931	0.80[CEU][hapmap]
rs4503768	1.00[CHB][hapmap]
rs4923840	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7172155	1.00[CHB][hapmap]
rs7173948	1.00[CHB][hapmap]
rs7181354	1.00[CHB][hapmap]
rs7182423	1.00[CHB][hapmap]
rs8041266	1.00[CHB][hapmap]
rs880270	1.00[CHB][hapmap]
rs937961	1.00[CHB][hapmap]
rs937962	1.00[CHB][hapmap]
rs9972350	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	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40076000-40103200	Weak transcription	Right Atrium	heart
2	chr15:40077600-40094600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:40080000-40095600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:40080400-40095000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:40081400-40100200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:40086000-40095600	Weak transcription	HUVEC	blood vessel
7	chr15:40088000-40095000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:40088800-40094600	Strong transcription	Osteobl	bone
9	chr15:40089600-40099400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:40090000-40094600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:40090400-40099000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:40090400-40099400	Strong transcription	NHLF	lung
13	chr15:40090600-40094600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:40091000-40102600	Weak transcription	Adipose Nuclei	Adipose
15	chr15:40091600-40095800	Weak transcription	HMEC	breast
16	chr15:40091800-40099400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:40092000-40094600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:40092000-40094600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:40092000-40095200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:40092200-40094600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:40092400-40095200	Weak transcription	Fetal Stomach	stomach
22	chr15:40092400-40096200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr15:40092600-40094600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:40092600-40094600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:40092600-40096000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr15:40092800-40098200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:40093200-40094600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:40094000-40096000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:40094000-40096200	Weak transcription	NH-A	brain
30	chr15:40094200-40100400	Weak transcription	Spleen	Spleen
31	chr15:40094400-40095800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:40094400-40095800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:40094400-40095800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:40094400-40095800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:40094400-40095800	Weak transcription	HSMM	muscle
36	chr15:40094400-40095800	Weak transcription	NHEK	skin
37	chr15:40094400-40096000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr15:40094400-40096000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:40094400-40096800	Weak transcription	NHDF-Ad	bronchial
40	chr15:40094400-40097400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:40094400-40097600	Weak transcription	Aorta	Aorta
42	chr15:40094400-40100000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:40094400-40100200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:40094400-40102400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:40094400-40109600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:40094400-40120400	Weak transcription	HSMMtube	muscle

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