Variant report

Variant	rs4493745
Chromosome Location	chr6:53593569-53593570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53593244..53593769-chr6:53820705..53821237,2	MCF-7	breast:
2	chr6:53375847..53377727-chr6:53591880..53594689,2	MCF-7	breast:
3	chr6:53593116..53596418-chr6:53657644..53660881,3	MCF-7	breast:
4	chr6:53357447..53358709-chr6:53592427..53594072,11	K562	blood:
5	chr6:53357659..53358540-chr6:53592973..53593762,2	MCF-7	breast:
6	chr6:53589302..53590903-chr6:53592714..53595336,2	K562	blood:
7	chr6:53592971..53596675-chr6:53657710..53661284,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs3000998	0.86[TSI][hapmap]
rs35709775	0.93[EUR][1000 genomes]
rs4269375	0.86[TSI][hapmap]
rs4421195	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4518484	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4715425	0.86[TSI][hapmap]
rs7738167	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7744954	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7756654	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7756771	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7756797	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7763012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7767443	0.82[TSI][hapmap]
rs9382239	0.86[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4493745	IL17A	cis	parietal	SCAN
rs4493745	FBXO9	cis	parietal	SCAN
rs4493745	C6orf142	cis	cerebellum	SCAN
rs4493745	HMGCLL1	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53588800-53594600	Enhancers	Placenta	Placenta
2	chr6:53589400-53594400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:53589600-53593600	Enhancers	HepG2	liver
4	chr6:53589800-53594800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:53589800-53595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:53589800-53595000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:53589800-53599400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:53590000-53595000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:53590200-53595000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:53591000-53596800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:53591000-53599000	Weak transcription	Stomach Mucosa	stomach
12	chr6:53591200-53595000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:53591200-53596600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:53591200-53599600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:53591200-53599800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:53591600-53599600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:53592200-53593600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:53592400-53593600	Enhancers	HSMM	muscle
19	chr6:53592400-53593600	Enhancers	HSMMtube	muscle
20	chr6:53592400-53593600	Enhancers	NH-A	brain
21	chr6:53592400-53593800	Enhancers	A549	lung
22	chr6:53592400-53593800	Enhancers	HMEC	breast
23	chr6:53592600-53593600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:53592600-53593600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:53592600-53593800	Enhancers	Placenta Amnion	Placenta Amnion
26	chr6:53592600-53593800	Enhancers	NHEK	skin
27	chr6:53592800-53593600	Active TSS	NHDF-Ad	bronchial
28	chr6:53592800-53596600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:53593000-53593600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:53593000-53593800	Enhancers	Dnd41	blood
31	chr6:53593000-53599800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:53593200-53593600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr6:53593200-53593600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr6:53593200-53593600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr6:53593200-53593600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr6:53593200-53593600	Enhancers	Primary B cells from peripheral blood	blood
37	chr6:53593200-53593600	Enhancers	Primary T cells from cord blood	blood
38	chr6:53593200-53593600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr6:53593200-53593600	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:53593200-53593600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:53593200-53593600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:53593200-53593600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr6:53593200-53593600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr6:53593200-53593600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:53593200-53593600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:53593200-53593600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:53593200-53593600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr6:53593200-53593600	Enhancers	Liver	Liver
49	chr6:53593200-53593600	Enhancers	Brain Anterior Caudate	brain
50	chr6:53593200-53593600	Flanking Active TSS	Brain Cingulate Gyrus	brain

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