Variant report

Variant	rs13116304
Chromosome Location	chr4:15569146-15569147
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10003739	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10008875	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10008889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10012838	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10017295	0.89[EUR][1000 genomes]
rs10020408	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10022610	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10025837	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10026851	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10030313	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10031017	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10034328	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10939621	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs10939628	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1134634	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs11932730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933521	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11939541	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11942335	0.87[EUR][1000 genomes]
rs11943107	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11945626	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12503015	0.88[EUR][1000 genomes]
rs12508186	0.94[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs12509029	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12511894	0.84[EUR][1000 genomes]
rs12640192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12644327	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12649803	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs13104845	0.86[ASN][1000 genomes]
rs13121363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473166	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16892140	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16892141	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs16892152	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041671	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2110361	0.88[ASN][1000 genomes]
rs2160044	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28419165	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28522268	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28528670	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28534607	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28661857	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822298	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4235380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs4279203	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs4280723	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4280724	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4393989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4583752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs4591601	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4642244	0.89[EUR][1000 genomes]
rs4698117	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4698403	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4698405	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4698408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56041141	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57526178	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59055524	0.88[ASN][1000 genomes]
rs60040560	0.81[EUR][1000 genomes]
rs60813847	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290565	0.88[ASN][1000 genomes]
rs62290605	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6449146	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]
rs6449147	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs6449149	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6831286	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6839438	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73125606	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73125616	0.86[EUR][1000 genomes]
rs73125627	0.88[EUR][1000 genomes]
rs73125637	0.88[EUR][1000 genomes]
rs73127647	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7377825	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs741180	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759212	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7661102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7665390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7665915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7682586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7687010	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7692607	0.81[ASN][1000 genomes]
rs7697314	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs872678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9996452	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13116304	BOD1L	cis	parietal	SCAN
rs13116304	CC2D2A	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
2	chr4:15502800-15577600	Weak transcription	Right Ventricle	heart
3	chr4:15512000-15580000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
5	chr4:15520000-15572400	Weak transcription	Small Intestine	intestine
6	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
7	chr4:15539000-15570400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:15543800-15570600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:15544800-15571600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:15544800-15576200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:15545000-15575600	Weak transcription	Fetal Heart	heart
12	chr4:15546000-15589600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:15546200-15569400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:15546400-15572600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:15546800-15569200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:15548800-15570800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:15549600-15570800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
19	chr4:15554000-15572800	Strong transcription	Fetal Brain Female	brain
20	chr4:15554600-15601400	Weak transcription	A549	lung
21	chr4:15555800-15569200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr4:15555800-15589400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:15556000-15569200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:15556000-15603200	Weak transcription	Fetal Thymus	thymus
25	chr4:15558400-15574600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:15559600-15579000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr4:15560200-15570200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:15560200-15571800	Weak transcription	HepG2	liver
29	chr4:15560200-15577400	Weak transcription	HSMMtube	muscle
30	chr4:15560200-15580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr4:15560400-15572000	Weak transcription	Stomach Mucosa	stomach
32	chr4:15561400-15572400	Strong transcription	Fetal Muscle Leg	muscle
33	chr4:15561600-15572600	Strong transcription	Fetal Stomach	stomach
34	chr4:15561800-15572400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:15561800-15572400	Strong transcription	Ovary	ovary
36	chr4:15562000-15573400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:15562200-15569800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:15562400-15570000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr4:15562400-15572400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr4:15562400-15573000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:15562600-15571200	Strong transcription	Left Ventricle	heart
42	chr4:15562600-15573000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:15562600-15574800	Strong transcription	Brain Germinal Matrix	brain
44	chr4:15563200-15572200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:15563600-15572200	Strong transcription	NHLF	lung
46	chr4:15563600-15576600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr4:15563800-15572800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:15563800-15573200	Strong transcription	Fetal Intestine Small	intestine
49	chr4:15564000-15572200	Strong transcription	Adipose Nuclei	Adipose
50	chr4:15564000-15572200	Strong transcription	Liver	Liver

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