Variant report

Variant	rs7681728
Chromosome Location	chr4:2680515-2680516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10937912	0.84[CHB][hapmap]
rs10937922	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11490068	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11726971	0.81[ASN][1000 genomes]
rs12499258	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12499320	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs12502642	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12503424	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12503560	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12506536	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12509102	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12509910	0.82[EUR][1000 genomes]
rs13118890	0.81[ASN][1000 genomes]
rs13145281	0.82[CHB][hapmap]
rs16843272	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs16843281	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs16843291	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17132645	0.91[MKK][hapmap]
rs17164088	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17164090	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17412860	0.91[CHB][hapmap]
rs17825119	0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1828803	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1913448	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2090082	0.82[ASN][1000 genomes]
rs2137835	0.81[CHB][hapmap]
rs2239726	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2269495	0.86[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap]
rs2282765	0.91[MKK][hapmap]
rs2282766	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2282767	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2282768	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2285082	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2295499	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs2298959	0.83[ASN][1000 genomes]
rs2298960	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2298961	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2298964	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298965	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2341303	0.86[CHB][hapmap]
rs34626871	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35424748	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35679952	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3733215	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3733222	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3733223	0.86[CHB][hapmap]
rs3749467	0.91[MKK][hapmap]
rs3775070	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3849666	0.91[MKK][hapmap]
rs3864117	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4039740	0.82[ASN][1000 genomes]
rs4690016	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4690028	0.82[ASN][1000 genomes]
rs4690029	0.80[ASN][1000 genomes]
rs4690032	0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs4690052	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4690053	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4690055	0.95[CHB][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs4690060	0.86[CHB][hapmap]
rs4690085	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4690086	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4690088	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4690089	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55641756	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55679022	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55688738	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55993221	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56026329	0.85[ASN][1000 genomes]
rs56803054	0.81[ASN][1000 genomes]
rs57978437	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59425183	0.82[ASN][1000 genomes]
rs59609182	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61790216	0.81[AMR][1000 genomes]
rs61790220	0.82[ASN][1000 genomes]
rs61790221	0.82[ASN][1000 genomes]
rs73189408	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73189410	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73189411	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73207343	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73207348	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73207352	0.88[ASN][1000 genomes]
rs762856	0.86[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap]
rs9683585	0.84[ASN][1000 genomes]
rs9683949	0.81[CHB][hapmap]
rs9761799	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9762293	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948659	chr4:1828867-2815632	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1003409	chr4:2541224-2724199	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv878443	chr4:2598799-2731331	Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1005116	chr4:2633935-2812340	Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv470001	chr4:2680515-2723531	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7681728	GAK	cis	parietal	SCAN
rs7681728	ZFYVE28	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2627200-2683600	Strong transcription	Fetal Thymus	thymus
2	chr4:2638200-2724400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:2662600-2685600	Weak transcription	Fetal Brain Male	brain
4	chr4:2669600-2692200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:2671200-2682400	Strong transcription	Liver	Liver
6	chr4:2673600-2714400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:2673800-2698000	Weak transcription	Fetal Heart	heart
8	chr4:2674200-2682000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:2674200-2685600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:2674200-2686400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:2674200-2695600	Weak transcription	Stomach Mucosa	stomach
12	chr4:2674600-2685600	Weak transcription	Brain Substantia Nigra	brain
13	chr4:2674800-2681800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:2674800-2683200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:2674800-2685800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:2674800-2685800	Weak transcription	HMEC	breast
17	chr4:2674800-2686400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:2675200-2682000	Weak transcription	Spleen	Spleen
19	chr4:2675200-2683200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:2675200-2685200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:2675200-2685800	Weak transcription	Pancreas	Pancrea
22	chr4:2675200-2685800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:2675200-2691600	Weak transcription	Small Intestine	intestine
24	chr4:2675200-2698200	Weak transcription	Psoas Muscle	Psoas
25	chr4:2675400-2685400	Weak transcription	HSMMtube	muscle
26	chr4:2675400-2685800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:2675400-2689200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr4:2675600-2686200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:2675600-2692000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:2676000-2685600	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:2676200-2684400	Weak transcription	HUVEC	blood vessel
32	chr4:2676200-2685600	Weak transcription	Brain Germinal Matrix	brain
33	chr4:2676200-2685600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:2676400-2685600	Weak transcription	Aorta	Aorta
35	chr4:2676400-2685600	Weak transcription	Lung	lung
36	chr4:2676400-2685600	Weak transcription	Right Ventricle	heart
37	chr4:2676400-2685800	Weak transcription	Esophagus	oesophagus
38	chr4:2676400-2685800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr4:2676400-2686200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:2676600-2685600	Weak transcription	Brain Anterior Caudate	brain
41	chr4:2677000-2685600	Weak transcription	Fetal Brain Female	brain
42	chr4:2677000-2685600	Weak transcription	Fetal Kidney	kidney
43	chr4:2677200-2682000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:2677200-2685600	Weak transcription	Brain Angular Gyrus	brain
45	chr4:2677200-2685600	Weak transcription	Left Ventricle	heart
46	chr4:2677200-2685600	Weak transcription	NH-A	brain
47	chr4:2677200-2685800	Weak transcription	Ovary	ovary
48	chr4:2677200-2692200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:2677400-2682200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr4:2677400-2685600	Weak transcription	Thymus	Thymus

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