Variant report

Variant	rs6815377
Chromosome Location	chr4:110547116-110547117
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10006897	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10010159	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10017027	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10020263	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs1029449	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1029450	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1029451	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1042891	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11098036	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11098039	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11098040	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11724306	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11937120	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12498588	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12504784	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs12511995	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12646055	0.80[CHB][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12647060	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13103167	0.80[CHD][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs13151303	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1476545	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs197203	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs197231	0.85[CEU][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs197235	0.81[ASN][1000 genomes]
rs2079131	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2107051	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2285712	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs28380238	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28850086	0.81[ASN][1000 genomes]
rs28892996	0.81[ASN][1000 genomes]
rs3181191	0.86[CEU][hapmap];0.91[GIH][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3182325	0.81[EUR][1000 genomes]
rs34925690	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35838666	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3733611	0.86[CEU][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3756256	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3796911	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3796912	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4698744	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4698745	0.81[EUR][1000 genomes]
rs4698748	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4698776	0.84[TSI][hapmap]
rs4698777	0.81[EUR][1000 genomes]
rs4698780	0.86[CEU][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59207576	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60916792	0.82[ASN][1000 genomes]
rs6533438	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533444	0.90[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6533445	0.86[CEU][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6816926	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6825095	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6831930	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6833490	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6834082	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6834701	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6849691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6851190	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6851356	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6856535	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs726583	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs726584	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs726585	0.86[CEU][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs735642	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7672819	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs767598	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7676806	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7699736	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9990765	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9993532	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9996648	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9996730	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv3419480	chr4:110521397-110549622	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6815377	LARP7	cis	parietal	SCAN
rs6815377	CASP6	cis	cerebellum	SCAN
rs6815377	SGMS2	cis	cerebellum	SCAN
rs6815377	ANK2	cis	cerebellum	SCAN
rs6815377	CASP6	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110531000-110550600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:110531600-110549600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:110533000-110573000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr4:110533400-110552800	Weak transcription	Primary B cells from cord blood	blood
5	chr4:110536000-110552800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr4:110536400-110552800	Weak transcription	Adipose Nuclei	Adipose
7	chr4:110536400-110552800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:110537400-110547200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:110538400-110552000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:110539400-110549200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:110539400-110550800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:110544200-110552800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:110544200-110552800	Weak transcription	Ovary	ovary
14	chr4:110545200-110552800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:110545400-110552800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:110546000-110547400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr4:110546000-110549000	Weak transcription	Primary T cells from cord blood	blood
18	chr4:110546000-110559600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:110546200-110548400	Weak transcription	Fetal Intestine Small	intestine
20	chr4:110546200-110548800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr4:110546200-110549200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:110546200-110549200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:110546200-110550800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:110546200-110550800	Weak transcription	Esophagus	oesophagus
25	chr4:110546200-110550800	Weak transcription	Placenta	Placenta
26	chr4:110546200-110551000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:110546200-110552000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:110546200-110552600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:110546200-110552600	Weak transcription	Fetal Intestine Large	intestine
30	chr4:110546200-110552800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:110546200-110552800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:110546200-110552800	Weak transcription	Small Intestine	intestine
33	chr4:110546200-110566400	Weak transcription	Fetal Thymus	thymus
34	chr4:110546400-110550600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr4:110546400-110552800	Weak transcription	Right Atrium	heart
36	chr4:110546600-110547200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr4:110546600-110547600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:110546600-110549400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:110546600-110580600	Weak transcription	Thymus	Thymus
40	chr4:110546800-110549600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:110547000-110547400	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr4:110547000-110548000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr4:110547000-110548600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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