Variant report

Variant	rs12924999
Chromosome Location	chr16:75262425-75262426
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75258373..75260591-chr16:75260652..75263277,2	K562	blood:
2	chr16:75261304..75263525-chr16:75287372..75289617,2	K562	blood:
3	chr16:75260096..75262598-chr16:75274071..75277051,2	K562	blood:
4	chr16:75261676..75264037-chr16:75269916..75271936,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000050820	Chromatin interaction
ENSG00000240338	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1019539	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs1035540	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10871304	0.85[CEU][hapmap]
rs1107593	0.92[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11149811	0.93[CEU][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11641896	0.96[EUR][1000 genomes]
rs12918452	0.82[EUR][1000 genomes]
rs1808427	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1862738	0.92[EUR][1000 genomes]
rs2870471	0.80[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2870472	0.93[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3169330	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4479268	0.85[CEU][hapmap]
rs4737	1.00[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs4888361	0.96[EUR][1000 genomes]
rs4888362	0.86[EUR][1000 genomes]
rs4888363	0.80[CEU][hapmap];0.92[EUR][1000 genomes]
rs4888364	0.95[EUR][1000 genomes]
rs4888365	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6564221	0.85[CEU][hapmap]
rs6564239	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6564241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6564243	0.96[EUR][1000 genomes]
rs7195938	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7202566	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8048371	0.96[EUR][1000 genomes]
rs8048956	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8057145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8059190	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8061356	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs889514	0.90[EUR][1000 genomes]
rs889515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9319481	0.84[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9927264	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9928842	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv1056082	chr16:75004990-75295847	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv833282	chr16:75154171-75330634	Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS 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	36 gene(s)	inside rSNPs	diseases
6	nsv516504	chr16:75223491-75306402	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523405	chr16:75227969-75342846	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	esv1806781	chr16:75235390-75307470	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv906909	chr16:75236154-75316074	Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	esv1792587	chr16:75237936-75305783	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv906910	chr16:75251299-75316074	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv906911	chr16:75252526-75296247	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv906912	chr16:75252526-75320827	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv1813349	chr16:75257361-75302684	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12924999	LRCH2	trans	cerebellum	SCAN
rs12924999	CNTNAP4	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75253200-75263400	Weak transcription	HSMMtube	muscle
2	chr16:75254000-75267600	Weak transcription	Fetal Brain Male	brain
3	chr16:75254600-75268000	Weak transcription	GM12878-XiMat	blood
4	chr16:75256400-75266600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr16:75256600-75263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr16:75256600-75267600	Weak transcription	Fetal Heart	heart
7	chr16:75256600-75267600	Weak transcription	Right Atrium	heart
8	chr16:75258800-75262800	Weak transcription	Fetal Lung	lung
9	chr16:75259000-75263200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr16:75259400-75267400	Weak transcription	Psoas Muscle	Psoas
11	chr16:75260000-75267800	Weak transcription	Stomach Mucosa	stomach
12	chr16:75260400-75263400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr16:75260600-75262800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr16:75260600-75263000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr16:75260600-75263600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr16:75260600-75264800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr16:75260800-75264000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr16:75260800-75266600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr16:75260800-75267600	Strong transcription	Fetal Intestine Small	intestine
20	chr16:75260800-75278000	Weak transcription	Small Intestine	intestine
21	chr16:75261000-75262600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr16:75261000-75263000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr16:75261000-75264000	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr16:75261000-75264200	Genic enhancers	Spleen	Spleen
25	chr16:75261000-75267000	Strong transcription	Fetal Stomach	stomach
26	chr16:75261000-75267200	Strong transcription	NHLF	lung
27	chr16:75261000-75267600	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr16:75261000-75267600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr16:75261000-75268000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr16:75261000-75268000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr16:75261200-75264800	Strong transcription	Brain Cingulate Gyrus	brain
32	chr16:75261200-75268000	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr16:75261400-75263000	Weak transcription	Hela-S3	cervix
34	chr16:75261400-75264000	Strong transcription	Fetal Brain Female	brain
35	chr16:75261400-75264000	Strong transcription	Left Ventricle	heart
36	chr16:75261400-75264200	Strong transcription	Brain Hippocampus Middle	brain
37	chr16:75261400-75264400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr16:75261400-75264800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr16:75261400-75265000	Strong transcription	Brain Germinal Matrix	brain
40	chr16:75261400-75267600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr16:75261400-75267800	Strong transcription	NHDF-Ad	bronchial
42	chr16:75261400-75268000	Strong transcription	Esophagus	oesophagus
43	chr16:75261400-75268000	Strong transcription	Gastric	stomach
44	chr16:75261400-75268000	Strong transcription	HUVEC	blood vessel
45	chr16:75261400-75271800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr16:75261400-75272400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr16:75261600-75263400	Strong transcription	Placenta	Placenta
48	chr16:75261600-75263400	Strong transcription	Lung	lung
49	chr16:75261600-75264000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr16:75261600-75264000	Strong transcription	Aorta	Aorta

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