Variant report

Variant	rs16971976
Chromosome Location	chr15:41989926-41989927
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	chr15:41950960..41953076-chr15:41988289..41990930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1107858	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11634956	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637341	0.93[ASN][1000 genomes]
rs12440747	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1531140	0.86[JPT][hapmap]
rs16952372	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17676742	0.93[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs17677199	0.93[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs17677991	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs17678138	0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs17678310	0.91[ASW][hapmap]
rs17678552	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs17734856	0.86[JPT][hapmap]
rs1918310	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2004162	0.93[ASN][1000 genomes]
rs2241522	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2277535	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2303516	0.85[JPT][hapmap]
rs2303518	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap]
rs2412622	0.92[ASN][1000 genomes]
rs2577960	0.82[ASN][1000 genomes]
rs28556632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700954	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28810086	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28850384	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743024	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs4923905	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs4924564	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs4924570	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4924576	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs62002066	0.93[ASN][1000 genomes]
rs62003900	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171123	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8035855	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9672298	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs9672360	1.00[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1048655	chr15:41978391-42049360	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16971976	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs16971976	JMJD7-PLA2G4B	cis	parietal	SCAN
rs16971976	C15orf41	cis	cerebellum	SCAN
rs16971976	ZSCAN29	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
2	chr15:41961800-41990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:41962000-41990800	Weak transcription	NH-A	brain
4	chr15:41962000-41991200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:41962000-42001400	Weak transcription	Gastric	stomach
6	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:41971600-41997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:41972800-41999600	Weak transcription	Fetal Brain Female	brain
10	chr15:41978800-41991200	Weak transcription	Liver	Liver
11	chr15:41981600-41995800	Weak transcription	Fetal Stomach	stomach
12	chr15:41983000-42001200	Weak transcription	Ovary	ovary
13	chr15:41983200-42002600	Weak transcription	Small Intestine	intestine
14	chr15:41984200-41990600	Weak transcription	Fetal Intestine Large	intestine
15	chr15:41984200-42034800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:41984400-42002800	Weak transcription	A549	lung
17	chr15:41984600-41991000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:41984600-41993000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:41984600-41999200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:41984600-41999400	Weak transcription	Thymus	Thymus
21	chr15:41984600-41999800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:41984600-42000600	Weak transcription	Lung	lung
23	chr15:41984600-42001600	Weak transcription	Pancreas	Pancrea
24	chr15:41984800-41991800	Weak transcription	Spleen	Spleen
25	chr15:41984800-41998800	Weak transcription	Left Ventricle	heart
26	chr15:41984800-41999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:41984800-42000800	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:41984800-42001200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:41984800-42001400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:41984800-42003000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:41985200-41996000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:41985600-41990800	Weak transcription	HSMM	muscle
33	chr15:41986000-41990600	Weak transcription	NHEK	skin
34	chr15:41987200-41990000	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr15:41987600-42001200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:41988200-41990800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:41988200-41991400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:41988200-41995000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:41988600-42001200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:41988600-42003000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:41988600-42003000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:41988800-41990000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:41988800-41990800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:41988800-41991200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr15:41988800-41994600	Strong transcription	Fetal Thymus	thymus
46	chr15:41988800-42002200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr15:41988800-42003000	Weak transcription	Fetal Kidney	kidney
48	chr15:41989000-41990000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr15:41989000-41991000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:41989000-41991200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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