Variant report

Variant	rs16971915
Chromosome Location	chr15:41914305-41914306
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	chr15:41913263..41914798-chr15:41951320..41953702,2	MCF-7	breast:
2	chr13:28195990..28196517-chr15:41913983..41914517,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction
ENSG00000186184	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1106934	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs11070349	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs11858843	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1197659	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs1197689	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap]
rs1197690	0.93[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap]
rs1197773	0.93[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12439488	0.84[AMR][1000 genomes]
rs12439771	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12440605	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs12591253	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12591285	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs12595271	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs12901742	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1918312	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1918313	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2077361	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2577949	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs34405276	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4072386	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4923906	1.00[CEU][hapmap]
rs4923907	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4924573	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7168386	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7173431	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7173779	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7174099	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7175346	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs7177495	0.93[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs8024907	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8038764	0.90[ASN][1000 genomes]
rs9788715	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9788733	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052902	chr15:41869277-41951572	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16971915	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs16971915	NUSAP1	cis	cerebellum	SCAN
rs16971915	VPS18	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41912600-41914400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:41912600-41915000	Active TSS	A549	lung
3	chr15:41912800-41914400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr15:41912800-41914400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr15:41912800-41914600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:41912800-41914600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr15:41912800-41914600	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr15:41912800-41914600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:41912800-41914600	Flanking Active TSS	HepG2	liver
10	chr15:41912800-41914800	Active TSS	Brain Anterior Caudate	brain
11	chr15:41912800-41915000	Active TSS	Fetal Brain Female	brain
12	chr15:41913000-41914400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr15:41913000-41914400	Active TSS	Aorta	Aorta
14	chr15:41913000-41914400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr15:41913000-41914600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:41913000-41914600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr15:41913000-41914600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:41913000-41914600	Active TSS	Brain Substantia Nigra	brain
19	chr15:41913000-41914600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr15:41913000-41914600	Active TSS	Ovary	ovary
21	chr15:41913000-41914600	Active TSS	Psoas Muscle	Psoas
22	chr15:41913000-41914600	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr15:41913000-41914600	Active TSS	Rectal Smooth Muscle	rectum
24	chr15:41913000-41914600	Active TSS	Right Atrium	heart
25	chr15:41913000-41914600	Active TSS	HSMM	muscle
26	chr15:41913000-41914600	Active TSS	HSMMtube	muscle
27	chr15:41913000-41914800	Active TSS	Brain Cingulate Gyrus	brain
28	chr15:41913200-41914400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:41913200-41914400	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr15:41913200-41914400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr15:41913200-41914400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr15:41913200-41914400	Active TSS	Fetal Heart	heart
33	chr15:41913200-41914600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:41913200-41914600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr15:41913200-41914600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
36	chr15:41913200-41914600	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr15:41913200-41914600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:41913200-41914600	Active TSS	Fetal Lung	lung
39	chr15:41913200-41914600	Flanking Active TSS	Placenta	Placenta
40	chr15:41913200-41914800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
41	chr15:41913200-41914800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr15:41913200-41914800	Active TSS	Brain Angular Gyrus	brain
43	chr15:41913200-41915000	Active TSS	Fetal Kidney	kidney
44	chr15:41913400-41914400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:41913400-41914600	Active TSS	Brain Germinal Matrix	brain
46	chr15:41913400-41914600	Active TSS	Brain Hippocampus Middle	brain
47	chr15:41913400-41914800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:41913400-41914800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:41913600-41914400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:41913600-41914400	Active TSS	Osteobl	bone

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