Variant report

Variant	rs4698780
Chromosome Location	chr4:110602430-110602431
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110592093..110594740-chr4:110602207..110604026,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10004377	0.88[LWK][hapmap]
rs10010159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10017027	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10020263	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10032323	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs1008326	0.82[JPT][hapmap]
rs1029449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1029450	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1029451	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1042891	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098039	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098040	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11724306	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728699	0.85[LWK][hapmap]
rs12498588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504296	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12504784	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12511995	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646055	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12647060	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103167	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112432	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13151303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476545	0.82[GIH][hapmap]
rs2079131	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2107050	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2107051	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285712	1.00[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28380238	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28850086	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28892996	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181187	0.88[LWK][hapmap]
rs3181191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3182325	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34925690	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35838666	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756256	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698744	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698745	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4698747	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4698748	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4698776	0.86[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4698777	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5030535	0.80[YRI][hapmap]
rs5030594	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5030606	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59207576	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60916792	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6533438	0.81[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs6533444	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533445	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815377	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]
rs6816926	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6825095	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6831930	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6833490	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6834082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6849691	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6851190	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6851356	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6856535	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs726583	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs726584	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs726585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs735642	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7439493	0.92[LWK][hapmap]
rs763370	0.95[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7672819	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674356	0.88[LWK][hapmap]
rs767598	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7694620	0.88[LWK][hapmap]
rs7699736	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7699969	0.81[TSI][hapmap]
rs9990765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9992400	0.83[LWK][hapmap]
rs9993532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9996648	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9996730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	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
2	nsv508303	chr4:110579305-110604452	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4698780	CASP6	cis	parietal	SCAN
rs4698780	FLJ20647	cis	multi-tissue	Pritchard
rs4698780	LARP7	cis	parietal	SCAN
rs4698780	COL25A1	cis	cerebellum	SCAN
rs4698780	CASP6	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110571000-110605400	Weak transcription	Left Ventricle	heart
2	chr4:110572600-110623200	Weak transcription	Esophagus	oesophagus
3	chr4:110579200-110608400	Weak transcription	Ovary	ovary
4	chr4:110583600-110605600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:110584200-110606000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:110584400-110608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:110585800-110608800	Weak transcription	Adipose Nuclei	Adipose
8	chr4:110586000-110605200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:110589600-110623200	Weak transcription	Brain Substantia Nigra	brain
10	chr4:110590200-110602600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:110590600-110606000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:110591200-110602600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:110591200-110608600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:110591600-110605000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:110592000-110611600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:110592800-110603800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:110593000-110608200	Weak transcription	Fetal Lung	lung
18	chr4:110593800-110611600	Weak transcription	K562	blood
19	chr4:110596600-110605600	Weak transcription	GM12878-XiMat	blood
20	chr4:110597000-110605800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr4:110597400-110605600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:110597600-110603600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:110598400-110608200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:110598600-110603600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:110598600-110610400	Weak transcription	HSMMtube	muscle
26	chr4:110598800-110611200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:110598800-110622800	Weak transcription	NHEK	skin
28	chr4:110599400-110611400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:110600000-110610600	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:110600000-110611400	Weak transcription	Spleen	Spleen
31	chr4:110600200-110603600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:110600200-110604800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:110600200-110613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:110600400-110610000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:110600400-110610200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:110600400-110611800	Weak transcription	NHDF-Ad	bronchial
37	chr4:110600600-110603600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr4:110600600-110611200	Weak transcription	HSMM	muscle
39	chr4:110600800-110602800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:110600800-110604400	Strong transcription	Primary T cells from cord blood	blood
41	chr4:110600800-110604800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:110600800-110605400	Weak transcription	Thymus	Thymus
43	chr4:110600800-110605600	Weak transcription	Fetal Thymus	thymus
44	chr4:110600800-110622600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr4:110601000-110602600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:110601000-110602800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:110601000-110606600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:110601000-110607400	Weak transcription	Fetal Stomach	stomach
49	chr4:110601000-110608400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr4:110601200-110610200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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