Variant report

Variant	rs2412716
Chromosome Location	chr15:42763373-42763374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42762017..42764640-chr8:90562337..90564364,2	MCF-7	breast:
2	chr15:42281447..42282357-chr15:42763191..42763948,2	K562	blood:

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs11070371	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11633276	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11856807	1.00[EUR][1000 genomes]
rs12102204	1.00[EUR][1000 genomes]
rs12441027	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12593511	1.00[EUR][1000 genomes]
rs12902924	1.00[EUR][1000 genomes]
rs12911561	1.00[EUR][1000 genomes]
rs1659214	1.00[EUR][1000 genomes]
rs1659216	1.00[EUR][1000 genomes]
rs1659220	0.86[GIH][hapmap];1.00[EUR][1000 genomes]
rs1659223	1.00[EUR][1000 genomes]
rs1659225	1.00[EUR][1000 genomes]
rs1678998	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1871156	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2244773	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289293	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2289297	1.00[EUR][1000 genomes]
rs2412683	1.00[EUR][1000 genomes]
rs2412684	1.00[EUR][1000 genomes]
rs2412689	1.00[EUR][1000 genomes]
rs2412694	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2412695	1.00[EUR][1000 genomes]
rs2412697	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2578651	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2595935	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2595938	1.00[ASN][1000 genomes]
rs2620372	1.00[EUR][1000 genomes]
rs28364379	1.00[EUR][1000 genomes]
rs28364398	1.00[EUR][1000 genomes]
rs28364400	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28364462	1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28364472	1.00[EUR][1000 genomes]
rs28364475	1.00[GIH][hapmap]
rs28364491	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28364495	1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28364498	1.00[EUR][1000 genomes]
rs28364500	1.00[EUR][1000 genomes]
rs28364503	1.00[ASW][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs28364504	1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs28364507	1.00[EUR][1000 genomes]
rs28364508	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs28364509	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28364511	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28364519	1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28364522	1.00[EUR][1000 genomes]
rs28364523	1.00[EUR][1000 genomes]
rs28364524	1.00[EUR][1000 genomes]
rs28364526	1.00[EUR][1000 genomes]
rs28364540	1.00[EUR][1000 genomes]
rs28364541	1.00[EUR][1000 genomes]
rs28364544	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28364557	1.00[EUR][1000 genomes]
rs28364559	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs28489155	1.00[EUR][1000 genomes]
rs28602748	0.80[ASN][1000 genomes]
rs28621687	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28726153	0.80[ASN][1000 genomes]
rs28745879	1.00[EUR][1000 genomes]
rs2899044	1.00[EUR][1000 genomes]
rs2899058	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3743002	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3803342	0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs4556762	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4923939	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4923941	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4924649	1.00[EUR][1000 genomes]
rs4924650	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4924657	1.00[EUR][1000 genomes]
rs4924668	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4924669	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4924670	1.00[EUR][1000 genomes]
rs4924671	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs5028173	1.00[EUR][1000 genomes]
rs62022303	0.80[ASN][1000 genomes]
rs62022305	0.80[ASN][1000 genomes]
rs6493034	1.00[EUR][1000 genomes]
rs6493038	1.00[EUR][1000 genomes]
rs6493041	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6493047	1.00[EUR][1000 genomes]
rs6493051	1.00[EUR][1000 genomes]
rs7164196	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7168121	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs7169553	1.00[EUR][1000 genomes]
rs7177193	1.00[EUR][1000 genomes]
rs7177463	1.00[EUR][1000 genomes]
rs7177521	1.00[EUR][1000 genomes]
rs7178396	1.00[EUR][1000 genomes]
rs7181940	1.00[EUR][1000 genomes]
rs7183399	1.00[EUR][1000 genomes]
rs8023568	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8023678	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs8036149	1.00[EUR][1000 genomes]
rs8036163	1.00[EUR][1000 genomes]
rs8037627	1.00[GIH][hapmap]
rs8040720	1.00[EUR][1000 genomes]
rs8042603	1.00[EUR][1000 genomes]
rs8043033	1.00[EUR][1000 genomes]
rs936603	1.00[EUR][1000 genomes]
rs9920851	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2412716	CCNDBP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42701200-42766600	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:42737200-42764800	Weak transcription	A549	lung
3	chr15:42744200-42767000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:42744200-42781800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:42744200-42782400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:42749600-42764600	Weak transcription	Colonic Mucosa	Colon
7	chr15:42750000-42782600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:42750200-42763600	Weak transcription	Right Atrium	heart
9	chr15:42750200-42766400	Weak transcription	Right Ventricle	heart
10	chr15:42750200-42782400	Weak transcription	Aorta	Aorta
11	chr15:42750400-42765000	Weak transcription	Fetal Brain Male	brain
12	chr15:42750600-42766800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:42750800-42763400	Weak transcription	Psoas Muscle	Psoas
14	chr15:42750800-42764400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:42750800-42782400	Weak transcription	Ovary	ovary
16	chr15:42751000-42782400	Weak transcription	Fetal Lung	lung
17	chr15:42753200-42764000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr15:42753600-42764000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:42754200-42764600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:42754600-42764600	Weak transcription	Small Intestine	intestine
21	chr15:42754600-42782400	Weak transcription	HSMMtube	muscle
22	chr15:42755000-42763600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:42756000-42777600	Weak transcription	Lung	lung
24	chr15:42756000-42782600	Weak transcription	Esophagus	oesophagus
25	chr15:42756200-42782400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:42756600-42763600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:42757800-42782600	Weak transcription	Gastric	stomach
28	chr15:42758000-42764800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:42758000-42781600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr15:42758000-42782400	Weak transcription	NHLF	lung
31	chr15:42758200-42764400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:42758200-42766200	Weak transcription	NH-A	brain
33	chr15:42758200-42766600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:42758200-42766600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:42758200-42770600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:42758200-42770800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:42758200-42776200	Weak transcription	HepG2	liver
38	chr15:42758200-42781600	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:42758200-42781600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:42758200-42781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr15:42758400-42763400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:42758400-42763600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:42758400-42764000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr15:42758400-42765000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:42758400-42765200	Weak transcription	Fetal Kidney	kidney
46	chr15:42758400-42766000	Weak transcription	Left Ventricle	heart
47	chr15:42758400-42766600	Weak transcription	Adipose Nuclei	Adipose
48	chr15:42758400-42766600	Weak transcription	Brain Angular Gyrus	brain
49	chr15:42758400-42775400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:42758400-42775400	Weak transcription	Spleen	Spleen

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