Variant report

Variant	rs28828764
Chromosome Location	chr7:55988679-55988680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10223916	0.85[JPT][hapmap]
rs10229446	0.94[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.87[ASN][1000 genomes]
rs10230845	0.85[JPT][hapmap]
rs10233558	0.85[JPT][hapmap]
rs10245725	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250964	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10252442	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266902	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10271662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277978	0.85[JPT][hapmap]
rs10435504	0.91[YRI][hapmap];0.87[ASN][1000 genomes]
rs11761352	0.90[JPT][hapmap];0.84[YRI][hapmap]
rs11765287	0.90[JPT][hapmap]
rs11765531	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11765577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241866	0.85[CHD][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap]
rs2135116	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2174461	0.90[JPT][hapmap]
rs28636652	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28678267	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28803557	0.85[JPT][hapmap]
rs34016595	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35844144	0.89[ASN][1000 genomes]
rs4275190	0.80[YRI][hapmap]
rs4470984	0.94[ASW][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4535700	0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4543497	0.94[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4577914	0.88[JPT][hapmap]
rs4689	0.94[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.87[ASN][1000 genomes]
rs4947533	0.94[ASW][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs4947534	0.84[YRI][hapmap]
rs4948096	0.94[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4948097	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4948099	0.85[ASN][1000 genomes]
rs57153841	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57251705	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60517461	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6593292	0.89[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6593294	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6593297	0.94[ASW][hapmap];0.80[YRI][hapmap]
rs66528253	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954499	0.85[ASN][1000 genomes]
rs6970827	0.90[CEU][hapmap]
rs6978852	0.85[JPT][hapmap]
rs73132854	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73132897	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73360358	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73360359	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7779394	0.85[JPT][hapmap]
rs7800001	0.85[ASN][1000 genomes]
rs9642405	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv427782	chr7:55703073-56010314	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
8	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
10	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
13	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
14	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv607034	chr7:55974028-56002247	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28828764	GBAS	cis	lymphoblastoid	seeQTL
rs28828764	SUMF2	cis	parietal	SCAN
rs28828764	GBAS	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:55955400-56004200	Weak transcription	Gastric	stomach
2	chr7:55956200-55990800	Weak transcription	Thymus	Thymus
3	chr7:55956200-56002200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:55956400-55990600	Weak transcription	Brain Anterior Caudate	brain
5	chr7:55956400-55995800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:55956400-55998800	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:55956600-55990800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:55962000-55990000	Weak transcription	HepG2	liver
9	chr7:55962000-55992800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:55967600-55995800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr7:55968600-55995000	Weak transcription	HSMM	muscle
12	chr7:55969800-55998200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:55971600-55993400	Weak transcription	Primary B cells from cord blood	blood
14	chr7:55971800-55992800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:55973600-55990800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:55974200-55994800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:55974400-55995600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:55974800-55993200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:55975000-56002000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:55975400-55995000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:55975600-55992800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:55975600-55992800	Weak transcription	Fetal Intestine Small	intestine
23	chr7:55975800-56006800	Weak transcription	Fetal Kidney	kidney
24	chr7:55976800-55994400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:55977200-55992400	Weak transcription	Small Intestine	intestine
26	chr7:55977200-55994400	Weak transcription	Hela-S3	cervix
27	chr7:55977800-55997600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:55978600-55995400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr7:55978800-55999400	Weak transcription	Placenta	Placenta
30	chr7:55979000-55994200	Weak transcription	NH-A	brain
31	chr7:55979400-55990600	Weak transcription	Fetal Heart	heart
32	chr7:55980000-55999000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr7:55980000-56001400	Weak transcription	Spleen	Spleen
34	chr7:55980200-55990800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:55980200-55991800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr7:55980400-56004000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr7:55980600-55990600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr7:55980600-55990800	Weak transcription	Brain Substantia Nigra	brain
39	chr7:55980600-55999400	Weak transcription	Psoas Muscle	Psoas
40	chr7:55980600-56001200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr7:55980600-56004200	Weak transcription	Right Ventricle	heart
42	chr7:55980800-55990600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr7:55980800-55991200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr7:55980800-55995400	Weak transcription	A549	lung
45	chr7:55980800-55999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr7:55981000-55993600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:55981200-55990600	Weak transcription	Aorta	Aorta
48	chr7:55981400-55990600	Weak transcription	Brain Angular Gyrus	brain
49	chr7:55981400-55990800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr7:55981400-55992600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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