Variant report

Variant	rs12899786
Chromosome Location	chr15:45469694-45469695
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45458776..45462841-chr15:45467209..45473486,10	K562	blood:
2	chr15:45458782..45460452-chr15:45469150..45471146,2	MCF-7	breast:
3	chr15:45459519..45461778-chr15:45469004..45470564,2	K562	blood:
4	chr15:45468204..45470159-chr15:45474606..45476155,2	K562	blood:

Variant related genes	Relation type
ENSG00000259539	Chromatin interaction
ENSG00000259519	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12323957	0.80[YRI][hapmap]
rs12438755	0.84[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12904079	0.86[EUR][1000 genomes]
rs12908943	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12913123	0.81[CEU][hapmap]
rs1648306	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs1648309	0.83[ASN][1000 genomes]
rs1648311	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs1648316	0.91[EUR][1000 genomes]
rs1648319	0.90[EUR][1000 genomes]
rs1706804	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs1706816	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs1706818	0.83[ASN][1000 genomes]
rs1706821	0.85[EUR][1000 genomes]
rs1706822	0.85[EUR][1000 genomes]
rs2256257	0.90[EUR][1000 genomes]
rs2292467	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2458236	1.00[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2467838	0.84[EUR][1000 genomes]
rs3959644	0.86[ASW][hapmap];0.95[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs60001836	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62026661	0.86[EUR][1000 genomes]
rs62026665	0.87[EUR][1000 genomes]
rs753414	0.88[TSI][hapmap]
rs8034761	0.83[EUR][1000 genomes]
rs8040896	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
6	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12899786	CTD-2651B20.1	cis	Artery Tibial	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45459800-45471800	Weak transcription	Small Intestine	intestine
2	chr15:45459800-45478000	Weak transcription	Aorta	Aorta
3	chr15:45460000-45471600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:45460000-45471800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:45460000-45472200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:45460000-45474800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:45460000-45477200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr15:45460000-45478600	Weak transcription	Thymus	Thymus
9	chr15:45460200-45478000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:45460400-45475200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:45460600-45471800	Weak transcription	Esophagus	oesophagus
12	chr15:45460600-45475400	Weak transcription	Brain Anterior Caudate	brain
13	chr15:45460600-45475600	Weak transcription	Left Ventricle	heart
14	chr15:45460600-45478000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr15:45460600-45478200	Weak transcription	Adipose Nuclei	Adipose
16	chr15:45461000-45471400	Weak transcription	Stomach Mucosa	stomach
17	chr15:45461200-45471800	Weak transcription	Pancreas	Pancrea
18	chr15:45461200-45473200	Weak transcription	Fetal Brain Male	brain
19	chr15:45461800-45471800	Strong transcription	Fetal Stomach	stomach
20	chr15:45462200-45477200	Weak transcription	Brain Hippocampus Middle	brain
21	chr15:45462400-45473600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:45462800-45471600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr15:45462800-45473800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:45463000-45473800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:45463200-45470200	Strong transcription	Ovary	ovary
26	chr15:45463200-45470400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:45463200-45470600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:45463200-45470600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:45463200-45470600	Strong transcription	Liver	Liver
30	chr15:45463200-45470600	Strong transcription	Brain Germinal Matrix	brain
31	chr15:45463200-45470800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:45463200-45471600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:45463200-45471600	Strong transcription	HepG2	liver
34	chr15:45463400-45470400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:45463600-45470400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:45463600-45470400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr15:45463600-45471600	Strong transcription	Fetal Brain Female	brain
38	chr15:45463800-45470400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:45464200-45471400	Weak transcription	HSMM	muscle
40	chr15:45464200-45472400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:45464600-45472400	Weak transcription	Colonic Mucosa	Colon
42	chr15:45465600-45471600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:45465800-45470400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:45466000-45478800	Weak transcription	Right Ventricle	heart
45	chr15:45466200-45471200	Weak transcription	Spleen	Spleen
46	chr15:45466200-45471600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:45466400-45471400	Weak transcription	HMEC	breast
48	chr15:45466400-45471600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:45466400-45477600	Weak transcription	Colon Smooth Muscle	Colon
50	chr15:45466600-45470200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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