Variant report

Variant	rs28488572
Chromosome Location	chr7:8053392-8053393
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10215645	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10226050	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10228900	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10229643	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10231036	0.91[AMR][1000 genomes]
rs10241457	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10243846	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10247928	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10248588	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10258788	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10273241	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10486205	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11984078	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12702692	0.85[ASN][1000 genomes]
rs12702693	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17568389	0.85[ASN][1000 genomes]
rs2079853	0.82[ASN][1000 genomes]
rs2109382	0.87[AMR][1000 genomes]
rs2191321	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2348774	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs258853	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28670736	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs37975	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs37977	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs37978	0.82[EUR][1000 genomes]
rs37981	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs37983	0.83[EUR][1000 genomes]
rs37988	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs37992	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs37994	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs37995	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs37998	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs37999	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs38001	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38002	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38003	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38004	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38006	0.88[AMR][1000 genomes]
rs38010	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs38011	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38012	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38013	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38014	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38016	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38017	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38018	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38019	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38021	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs38022	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38023	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720761	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4725057	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4725060	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62433404	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7785493	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9692283	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[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	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	84 gene(s)	inside rSNPs	diseases
2	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28488572	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8036400-8077400	Weak transcription	Right Ventricle	heart
2	chr7:8036600-8053800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr7:8036600-8057200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:8036600-8064400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:8036600-8064400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:8036600-8074600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:8038000-8066000	Weak transcription	Pancreas	Pancrea
8	chr7:8038400-8066000	Weak transcription	Spleen	Spleen
9	chr7:8041600-8053800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:8041600-8064400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:8041600-8095000	Weak transcription	Gastric	stomach
12	chr7:8041800-8075400	Weak transcription	Brain Hippocampus Middle	brain
13	chr7:8042800-8064400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:8043000-8099200	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:8043600-8068400	Weak transcription	NH-A	brain
16	chr7:8043800-8064400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr7:8043800-8064600	Weak transcription	Small Intestine	intestine
18	chr7:8044000-8062600	Weak transcription	Fetal Intestine Small	intestine
19	chr7:8044200-8063800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr7:8044200-8066000	Weak transcription	Lung	lung
21	chr7:8044600-8074400	Weak transcription	Brain Angular Gyrus	brain
22	chr7:8044800-8064400	Weak transcription	Aorta	Aorta
23	chr7:8045200-8066000	Weak transcription	Fetal Brain Male	brain
24	chr7:8046800-8053400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr7:8046800-8053800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr7:8046800-8054200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr7:8046800-8062800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr7:8046800-8064200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:8046800-8064400	Weak transcription	Ovary	ovary
30	chr7:8046800-8066000	Weak transcription	Left Ventricle	heart
31	chr7:8046800-8074400	Weak transcription	Brain Substantia Nigra	brain
32	chr7:8047000-8062200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:8047000-8064000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr7:8047000-8066000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr7:8047200-8054000	Weak transcription	Primary T cells from cord blood	blood
36	chr7:8047200-8059200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:8047200-8062200	Weak transcription	Brain Anterior Caudate	brain
38	chr7:8047200-8062200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr7:8047200-8063800	Weak transcription	Fetal Lung	lung
40	chr7:8047200-8064000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:8047200-8064000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr7:8047200-8064000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:8047200-8064400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr7:8047200-8065200	Weak transcription	Fetal Kidney	kidney
45	chr7:8047200-8065400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:8047200-8066000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr7:8047200-8066200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr7:8047400-8062400	Weak transcription	Brain Germinal Matrix	brain
49	chr7:8047400-8063400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr7:8047400-8063400	Weak transcription	Stomach Smooth Muscle	stomach

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