Variant report

Variant	rs2912209
Chromosome Location	chr15:72575735-72575736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72575298..72576860-chr15:72578215..72580118,2	K562	blood:

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10220917	1.00[CHB][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs10851849	1.00[EUR][1000 genomes]
rs11072348	1.00[EUR][1000 genomes]
rs11072352	1.00[EUR][1000 genomes]
rs11072372	1.00[ASN][1000 genomes]
rs12324592	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs12439127	1.00[ASN][1000 genomes]
rs12442820	1.00[CHB][hapmap]
rs12593333	1.00[EUR][1000 genomes]
rs12903688	1.00[EUR][1000 genomes]
rs12903882	1.00[ASN][1000 genomes]
rs13379855	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1457030	1.00[EUR][1000 genomes]
rs1598714	1.00[EUR][1000 genomes]
rs16953788	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16956667	1.00[ASN][1000 genomes]
rs16956675	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16956759	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16956826	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16956904	1.00[CHB][hapmap]
rs1800431	1.00[EUR][1000 genomes]
rs1816645	1.00[ASN][1000 genomes]
rs1963894	1.00[ASN][1000 genomes]
rs2162236	0.88[MEX][hapmap]
rs2415131	1.00[EUR][1000 genomes]
rs28393893	1.00[ASN][1000 genomes]
rs28408413	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28422889	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28439115	1.00[ASN][1000 genomes]
rs28471053	1.00[ASN][1000 genomes]
rs28488862	1.00[ASN][1000 genomes]
rs28541481	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2856926	1.00[EUR][1000 genomes]
rs2912208	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912211	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912212	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912213	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912218	1.00[EUR][1000 genomes]
rs2912221	0.88[MEX][hapmap]
rs2912222	0.84[ASW][hapmap];0.83[YRI][hapmap]
rs2912224	0.84[ASW][hapmap];0.83[YRI][hapmap]
rs2912232	1.00[EUR][1000 genomes]
rs2925647	1.00[EUR][1000 genomes]
rs2925651	1.00[EUR][1000 genomes]
rs2929516	1.00[EUR][1000 genomes]
rs2929520	1.00[EUR][1000 genomes]
rs2957367	1.00[EUR][1000 genomes]
rs2957370	1.00[EUR][1000 genomes]
rs2957371	1.00[EUR][1000 genomes]
rs2957722	1.00[EUR][1000 genomes]
rs2959901	1.00[EUR][1000 genomes]
rs2959902	1.00[EUR][1000 genomes]
rs2959905	1.00[EUR][1000 genomes]
rs2959907	1.00[EUR][1000 genomes]
rs2959916	0.83[YRI][hapmap]
rs2959919	0.83[YRI][hapmap]
rs2959920	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs2959925	0.88[MEX][hapmap]
rs2959928	1.00[EUR][1000 genomes]
rs2959933	0.84[ASW][hapmap];0.83[YRI][hapmap]
rs2959934	1.00[EUR][1000 genomes]
rs2959935	0.83[YRI][hapmap]
rs2959936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959937	1.00[EUR][1000 genomes]
rs2959940	0.96[AMR][1000 genomes]
rs2959942	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35293819	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35514603	1.00[EUR][1000 genomes]
rs4238451	1.00[EUR][1000 genomes]
rs4265763	1.00[EUR][1000 genomes]
rs4461029	1.00[EUR][1000 genomes]
rs4776587	1.00[EUR][1000 genomes]
rs4776588	1.00[EUR][1000 genomes]
rs4776593	0.88[MEX][hapmap]
rs4777487	1.00[EUR][1000 genomes]
rs4777493	1.00[EUR][1000 genomes]
rs4777501	0.88[MEX][hapmap]
rs4777502	1.00[EUR][1000 genomes]
rs6494988	1.00[EUR][1000 genomes]
rs6494989	1.00[EUR][1000 genomes]
rs6494995	1.00[EUR][1000 genomes]
rs6495002	1.00[CHB][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs7170173	1.00[EUR][1000 genomes]
rs7171097	1.00[EUR][1000 genomes]
rs7173348	1.00[EUR][1000 genomes]
rs7173532	1.00[EUR][1000 genomes]
rs7177512	1.00[EUR][1000 genomes]
rs7179691	1.00[EUR][1000 genomes]
rs7180934	1.00[EUR][1000 genomes]
rs73440555	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73440562	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73440566	1.00[ASN][1000 genomes]
rs73440586	1.00[ASN][1000 genomes]
rs73442510	1.00[ASN][1000 genomes]
rs8031658	1.00[EUR][1000 genomes]
rs8034892	1.00[EUR][1000 genomes]
rs8037749	1.00[EUR][1000 genomes]
rs8039489	1.00[ASN][1000 genomes]
rs8192349	1.00[ASN][1000 genomes]
rs8192419	1.00[ASN][1000 genomes]
rs8192422	1.00[ASN][1000 genomes]
rs930871	1.00[EUR][1000 genomes]
rs9672916	0.86[MEX][hapmap]
rs9806212	1.00[CHB][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9806258	1.00[ASN][1000 genomes]
rs9806374	1.00[CHB][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs998225	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
4	nsv1601	chr15:72549885-72585176	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv3494908	chr15:72570698-72576646	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
6	esv3494909	chr15:72571098-72576596	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
7	esv3494906	chr15:72571458-72576046	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	esv16227	chr15:72571691-72575838	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2912209	NBPF4	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72566000-72575800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:72566000-72576400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:72566000-72577800	Weak transcription	Fetal Intestine Small	intestine
4	chr15:72566000-72582400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:72566000-72611400	Weak transcription	Right Ventricle	heart
6	chr15:72566200-72577000	Weak transcription	Ovary	ovary
7	chr15:72566200-72577600	Weak transcription	Brain Angular Gyrus	brain
8	chr15:72566200-72578400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:72566200-72579200	Weak transcription	Primary T cells from cord blood	blood
10	chr15:72567000-72611800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:72567800-72581400	Weak transcription	Fetal Muscle Leg	muscle
12	chr15:72569000-72576800	Weak transcription	HSMMtube	muscle
13	chr15:72573000-72582600	Weak transcription	Placenta	Placenta
14	chr15:72573200-72575800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:72573200-72603000	Weak transcription	Fetal Intestine Large	intestine
16	chr15:72573400-72582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:72573600-72578600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:72573800-72575800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:72573800-72578600	Weak transcription	Adipose Nuclei	Adipose
20	chr15:72573800-72595000	Weak transcription	Brain Hippocampus Middle	brain
21	chr15:72573800-72595000	Weak transcription	Brain Substantia Nigra	brain
22	chr15:72573800-72596200	Weak transcription	Liver	Liver
23	chr15:72573800-72597200	Weak transcription	Brain Anterior Caudate	brain
24	chr15:72574400-72595000	Weak transcription	Lung	lung
25	chr15:72574600-72575800	Weak transcription	GM12878-XiMat	blood
26	chr15:72574600-72581000	Weak transcription	Fetal Brain Female	brain
27	chr15:72574800-72576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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