Variant report

Variant	rs4689572
Chromosome Location	chr4:7010504-7010505
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	chr4:7000584..7003824-chr4:7009123..7012546,3	MCF-7	breast:
2	chr4:7004705..7009453-chr4:7009806..7014166,7	K562	blood:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10009332	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10013211	0.85[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10013696	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10015163	0.96[CEU][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10019256	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10022657	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[YRI][hapmap]
rs10022869	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10032908	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs10155208	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10804990	0.82[JPT][hapmap]
rs10937762	0.82[JPT][hapmap]
rs10937763	0.82[JPT][hapmap]
rs10937771	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10937778	0.81[CHB][hapmap]
rs10937779	0.80[CHB][hapmap]
rs12119	0.80[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs12512922	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12648134	0.80[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12650200	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12650264	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13140943	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17742611	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17743234	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2301820	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2301821	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28380685	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34173965	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35490604	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35772786	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3756255	0.81[JPT][hapmap]
rs3857168	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3857169	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3857170	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3857172	0.87[ASN][1000 genomes]
rs3857173	0.85[ASN][1000 genomes]
rs3892145	0.96[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3892976	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4234790	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4315786	0.92[CEU][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4346651	0.82[JPT][hapmap]
rs4484301	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4689558	0.82[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs4689571	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56307635	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6831368	0.82[JPT][hapmap]
rs6834007	0.82[AMR][1000 genomes]
rs7670187	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7672632	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9291123	0.81[CHD][hapmap]
rs9790586	0.82[JPT][hapmap]
rs9999127	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv593547	chr4:7002344-7032180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv469847	chr4:7003525-7168441	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv878531	chr4:7006541-7129556	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv878532	chr4:7010504-7055603	Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4689572	GRPEL1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6991000-7021800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:6994000-7035600	Strong transcription	Fetal Stomach	stomach
3	chr4:6994000-7043200	Weak transcription	Right Atrium	heart
4	chr4:6994200-7035400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:6994400-7013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:6994600-7021400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:6995000-7020800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:6995400-7013600	Strong transcription	Fetal Thymus	thymus
9	chr4:6995800-7032800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:6996000-7014800	Strong transcription	Primary B cells from peripheral blood	blood
11	chr4:6996000-7035200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:6996400-7034800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:6996600-7021400	Strong transcription	Brain Germinal Matrix	brain
14	chr4:6997800-7013800	Strong transcription	Thymus	Thymus
15	chr4:7000200-7021600	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:7000600-7034400	Strong transcription	Dnd41	blood
17	chr4:7001200-7010600	Weak transcription	Fetal Heart	heart
18	chr4:7001200-7010800	Weak transcription	Small Intestine	intestine
19	chr4:7001400-7034600	Strong transcription	Primary T cells from cord blood	blood
20	chr4:7001600-7017200	Strong transcription	Placenta	Placenta
21	chr4:7001600-7035200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr4:7001600-7035400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr4:7001800-7020000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:7001800-7029000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr4:7001800-7035000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:7002000-7034400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr4:7002200-7020600	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:7002200-7035400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:7002400-7034400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:7003400-7013800	Strong transcription	Spleen	Spleen
31	chr4:7003600-7032600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:7003800-7010600	Weak transcription	Ovary	ovary
33	chr4:7004000-7010600	Weak transcription	Pancreas	Pancrea
34	chr4:7004000-7014800	Weak transcription	Fetal Lung	lung
35	chr4:7004400-7011600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:7004400-7016200	Weak transcription	Fetal Kidney	kidney
37	chr4:7005200-7010600	Strong transcription	Fetal Muscle Leg	muscle
38	chr4:7005400-7012400	Weak transcription	HUVEC	blood vessel
39	chr4:7006000-7010800	Weak transcription	Esophagus	oesophagus
40	chr4:7006000-7015400	Strong transcription	HSMM	muscle
41	chr4:7006200-7010600	Weak transcription	Brain Angular Gyrus	brain
42	chr4:7006200-7010800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr4:7006400-7012400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:7006400-7014800	Weak transcription	Right Ventricle	heart
45	chr4:7006400-7016000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:7006600-7010600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr4:7006600-7010600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr4:7006600-7011000	Weak transcription	HSMMtube	muscle
49	chr4:7006600-7021800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:7006800-7010800	Weak transcription	NH-A	brain

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