Variant report

Variant	rs748245
Chromosome Location	chr15:40629317-40629318
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40628035..40631006-chr15:40631506..40634762,3	MCF-7	breast:
2	chr15:40628661..40629604-chr15:40811567..40812516,2	K562	blood:
3	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:
4	chr15:40625172..40629583-chr15:40631432..40633911,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf52-3	chr15:40628760-40629647	NONHSAT041829

Variant related genes	Relation type
ENSG00000188549	Chromatin interaction
ENSG00000259330	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1077476	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11070264	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12081	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2118961	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2289333	0.85[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4334271	0.85[JPT][hapmap]
rs4923864	0.86[ASN][1000 genomes]
rs4924455	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7164564	0.82[ASN][1000 genomes]
rs7164747	0.82[ASN][1000 genomes]
rs7173747	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs882829	0.82[CHB][hapmap]
rs934937	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs748245	IVD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40617200-40630200	Weak transcription	A549	lung
2	chr15:40619600-40630400	Enhancers	Primary hematopoietic stem cells	blood
3	chr15:40620800-40629600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:40621000-40630200	Weak transcription	HepG2	liver
5	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
6	chr15:40621200-40633400	Weak transcription	Fetal Kidney	kidney
7	chr15:40621400-40629800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:40622400-40633800	Enhancers	Spleen	Spleen
9	chr15:40623000-40629400	Weak transcription	Brain Substantia Nigra	brain
10	chr15:40623000-40630600	Weak transcription	Aorta	Aorta
11	chr15:40623200-40629600	Weak transcription	Ovary	ovary
12	chr15:40623200-40630200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40623400-40630200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:40623800-40630600	Enhancers	Fetal Thymus	thymus
15	chr15:40624200-40630400	Weak transcription	Brain Angular Gyrus	brain
16	chr15:40624200-40630600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:40625000-40629600	Genic enhancers	Fetal Muscle Leg	muscle
18	chr15:40625800-40630000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:40625800-40630400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:40625800-40630600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr15:40625800-40630600	Enhancers	NHDF-Ad	bronchial
22	chr15:40625800-40631600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr15:40625800-40642800	Enhancers	Fetal Intestine Large	intestine
24	chr15:40626000-40629400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:40626000-40630000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr15:40626400-40629600	Genic enhancers	Pancreas	Pancrea
27	chr15:40626400-40629800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:40626400-40629800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:40626400-40629800	Weak transcription	Psoas Muscle	Psoas
30	chr15:40626400-40630400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:40626400-40631600	Enhancers	Adipose Nuclei	Adipose
32	chr15:40626600-40630000	Weak transcription	Fetal Brain Male	brain
33	chr15:40626600-40630000	Genic enhancers	Fetal Stomach	stomach
34	chr15:40626600-40630000	Genic enhancers	Right Ventricle	heart
35	chr15:40626600-40631800	Enhancers	Duodenum Mucosa	Duodenum
36	chr15:40626600-40633800	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr15:40626800-40629800	Genic enhancers	NHEK	skin
38	chr15:40626800-40630000	Genic enhancers	Lung	lung
39	chr15:40627000-40630000	Weak transcription	Stomach Mucosa	stomach
40	chr15:40627000-40630200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr15:40627000-40630400	Weak transcription	Fetal Brain Female	brain
42	chr15:40627000-40630800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:40627000-40632200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr15:40627000-40633400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:40627200-40629600	Strong transcription	Gastric	stomach
46	chr15:40627200-40629600	Genic enhancers	Rectal Smooth Muscle	rectum
47	chr15:40627200-40629800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr15:40627200-40629800	Strong transcription	NHLF	lung
49	chr15:40627200-40630000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:40627200-40630000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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