Variant report

Variant	rs12899266
Chromosome Location	chr15:43439786-43439787
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43423971..43426315-chr15:43439637..43441857,2	MCF-7	breast:
2	chr15:43398228..43401144-chr15:43439488..43441980,2	K562	blood:
3	chr15:43414412..43417295-chr15:43437126..43440064,2	K562	blood:

Variant related genes	Relation type
ENSG00000159459	Chromatin interaction
ENSG00000137842	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11070386	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs11070391	1.00[CEU][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11070396	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070397	0.83[EUR][1000 genomes]
rs11070398	0.91[EUR][1000 genomes]
rs11630595	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs11855754	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12592725	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1462856	1.00[CEU][hapmap]
rs16957511	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1834643	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2037392	0.82[CEU][hapmap]
rs2042742	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241516	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2412752	0.86[JPT][hapmap]
rs28585036	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs28756768	0.92[EUR][1000 genomes]
rs2899077	0.89[CEU][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes]
rs2947019	0.89[CEU][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34646108	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3736054	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs3784267	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3784268	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4573908	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs4923955	1.00[CEU][hapmap]
rs4924704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4924709	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs494863	0.89[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs495286	0.89[CEU][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs497138	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs499280	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs530305	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs531850	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs538218	0.89[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes]
rs540587	1.00[CEU][hapmap];0.94[JPT][hapmap];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6493076	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs6493077	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs6493078	0.95[ASN][1000 genomes]
rs7174915	1.00[CEU][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7176116	0.81[ASN][1000 genomes]
rs7183814	0.89[CEU][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes]
rs8027371	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8027733	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs8036710	0.81[ASN][1000 genomes]
rs8037022	1.00[CEU][hapmap]
rs8042481	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
9	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	esv1802035	chr15:43370916-43487742	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12899266	CCNDBP1	cis	Lymphoblastoid	GTEx
rs12899266	CCNDBP1	cis	multi-tissue	Pritchard
rs12899266	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43426600-43442200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:43426800-43455800	Weak transcription	Fetal Lung	lung
3	chr15:43426800-43465400	Weak transcription	Psoas Muscle	Psoas
4	chr15:43427000-43440600	Weak transcription	Fetal Heart	heart
5	chr15:43427000-43442200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:43427000-43442200	Weak transcription	NH-A	brain
7	chr15:43427600-43475000	Weak transcription	Stomach Mucosa	stomach
8	chr15:43427800-43448400	Weak transcription	Fetal Kidney	kidney
9	chr15:43428000-43445600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:43429400-43444400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:43430400-43441000	Weak transcription	HSMMtube	muscle
12	chr15:43430600-43441200	Weak transcription	Hela-S3	cervix
13	chr15:43430600-43442000	Weak transcription	HMEC	breast
14	chr15:43431000-43442000	Weak transcription	Fetal Thymus	thymus
15	chr15:43432200-43441000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:43432200-43446400	Weak transcription	Small Intestine	intestine
17	chr15:43433000-43441000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:43433200-43441000	Weak transcription	Colonic Mucosa	Colon
19	chr15:43433200-43460600	Weak transcription	Right Ventricle	heart
20	chr15:43433400-43440800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:43433400-43441200	Weak transcription	Brain Angular Gyrus	brain
22	chr15:43433400-43441200	Weak transcription	Lung	lung
23	chr15:43433400-43441800	Weak transcription	Aorta	Aorta
24	chr15:43433400-43441800	Weak transcription	Osteobl	bone
25	chr15:43433400-43442000	Weak transcription	NHLF	lung
26	chr15:43433400-43442400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:43433400-43442400	Weak transcription	NHEK	skin
28	chr15:43433400-43443600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr15:43433400-43446000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:43433400-43446000	Weak transcription	Ovary	ovary
31	chr15:43433400-43451800	Weak transcription	Esophagus	oesophagus
32	chr15:43433400-43452600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:43433400-43460400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:43433400-43460400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:43433400-43460400	Weak transcription	Spleen	Spleen
36	chr15:43433400-43460600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:43433400-43460600	Weak transcription	Gastric	stomach
38	chr15:43433400-43467600	Weak transcription	HSMM	muscle
39	chr15:43433600-43441000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:43433600-43441200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:43433600-43442400	Weak transcription	HepG2	liver
42	chr15:43433600-43442600	Weak transcription	Left Ventricle	heart
43	chr15:43433600-43444600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:43433600-43445400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr15:43433600-43447000	Weak transcription	Fetal Stomach	stomach
46	chr15:43433600-43447800	Weak transcription	Brain Substantia Nigra	brain
47	chr15:43433600-43460400	Weak transcription	Pancreas	Pancrea
48	chr15:43433600-43460400	Weak transcription	Thymus	Thymus
49	chr15:43433800-43440800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:43433800-43442400	Weak transcription	Fetal Muscle Leg	muscle

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