Variant report

Variant	rs4698776
Chromosome Location	chr4:110590821-110590822
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	chr4:110578534..110580904-chr4:110588408..110591184,2	K562	blood:
2	chr4:110582184..110585367-chr4:110588932..110592046,3	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10010159	0.86[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10020263	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032323	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1008326	0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1029449	0.86[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1029450	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1029451	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1042891	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11098039	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11098040	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11724306	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11931318	0.95[ASN][1000 genomes]
rs12498588	0.81[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12504296	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504784	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs12511995	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12646055	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12647060	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13103167	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13112432	0.85[EUR][1000 genomes]
rs13151303	0.86[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2079131	0.80[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2107050	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2107051	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2285712	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28380238	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28850086	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28892996	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3181191	0.86[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3182325	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34925690	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35838666	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3733611	0.86[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3756256	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3796911	0.86[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3796912	0.86[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4698744	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4698745	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698747	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698748	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698777	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4698780	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]
rs5030594	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5030606	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs59207576	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6533438	0.85[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]
rs6533444	0.81[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6533445	0.86[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6815377	0.84[TSI][hapmap]
rs6816926	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6825095	0.84[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6831930	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6833490	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6834082	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6834701	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6851190	0.86[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6851356	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6856535	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs726583	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs726584	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs726585	0.86[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs735642	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs763370	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672819	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs767598	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699736	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7699969	0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9990765	0.86[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9993532	0.86[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9996648	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9996730	0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4698776	FLJ20647	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

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	chr4:110574200-110592600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:110574200-110598400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:110579200-110608400	Weak transcription	Ovary	ovary
6	chr4:110581600-110596800	Weak transcription	Lung	lung
7	chr4:110583000-110596600	Weak transcription	HepG2	liver
8	chr4:110583600-110605600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:110584200-110591800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:110584200-110606000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:110584400-110591400	Weak transcription	GM12878-XiMat	blood
12	chr4:110584400-110608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:110585000-110592600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:110585200-110596800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:110585200-110599600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:110585400-110591800	Weak transcription	Thymus	Thymus
17	chr4:110585800-110591600	Weak transcription	Primary B cells from cord blood	blood
18	chr4:110585800-110591600	Weak transcription	Dnd41	blood
19	chr4:110585800-110608800	Weak transcription	Adipose Nuclei	Adipose
20	chr4:110586000-110591600	Weak transcription	Fetal Thymus	thymus
21	chr4:110586000-110599800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:110586000-110605200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:110586200-110591400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:110586200-110591800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:110586400-110591400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr4:110586600-110591200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr4:110586600-110591400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr4:110587800-110591600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:110588000-110591400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr4:110588000-110592000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:110588200-110593000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:110589000-110591600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr4:110589200-110591200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr4:110589200-110591400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr4:110589600-110623200	Weak transcription	Brain Substantia Nigra	brain
36	chr4:110589800-110591200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr4:110590200-110602600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:110590600-110591000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:110590600-110606000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:110590800-110591200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:110590800-110592000	Weak transcription	Primary T cells from cord blood	blood
42	chr4:110590800-110592000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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