Variant report

Variant	rs17654449
Chromosome Location	chr15:38991164-38991165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:38987442..38989993-chr15:38990794..38993577,2	MCF-7	breast:
2	chr15:38778715..38781483-chr15:38990694..38992879,2	MCF-7	breast:
3	chr15:38939213..38941167-chr15:38988952..38991433,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175779	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10459669	0.94[CEU][hapmap]
rs16967167	0.82[CEU][hapmap]
rs2172836	0.98[ASN][1000 genomes]
rs56081681	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17654449	IVD	cis	parietal	SCAN
rs17654449	C15orf54	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38986600-38992600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr15:38986600-38992600	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr15:38986800-38992400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr15:38986800-38992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:38987000-38992000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:38987200-38991800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr15:38987200-38992000	Enhancers	Primary hematopoietic stem cells	blood
8	chr15:38987200-38992400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr15:38987200-38992600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr15:38987800-38991400	Enhancers	Dnd41	blood
11	chr15:38987800-38991800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:38987800-38991800	Enhancers	Fetal Thymus	thymus
13	chr15:38988400-38992000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr15:38988600-38992400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:38988600-38994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:38989000-38997400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:38989000-38997600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:38989000-38997600	Weak transcription	HSMM	muscle
19	chr15:38989200-38992800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:38989400-38992600	Enhancers	Primary T cells fromperipheralblood	blood
21	chr15:38989400-38992800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:38989600-38992600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:38989800-38992400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr15:38989800-38992600	Enhancers	Primary T cells from cord blood	blood
25	chr15:38990000-38991400	Enhancers	Thymus	Thymus
26	chr15:38990400-38991600	Enhancers	Fetal Intestine Small	intestine
27	chr15:38990800-38991800	Enhancers	Fetal Intestine Large	intestine
28	chr15:38991000-38992000	Enhancers	Duodenum Mucosa	Duodenum
29	chr15:38991000-38992600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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