Variant report

Variant	rs2079853
Chromosome Location	chr7:8104099-8104100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10215645	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10226050	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10228900	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10229643	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10231036	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10241457	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10243846	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10247928	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10248588	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10258788	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10273241	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10486205	0.82[ASN][1000 genomes]
rs10486207	0.80[ASN][1000 genomes]
rs11976862	0.89[AFR][1000 genomes]
rs11984078	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702692	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12702693	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17568389	0.93[ASN][1000 genomes]
rs2109382	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2191321	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2348774	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs258853	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28488572	0.82[ASN][1000 genomes]
rs28670736	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs37975	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs37981	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs37988	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs37995	0.80[AMR][1000 genomes]
rs37998	0.81[AMR][1000 genomes]
rs37999	0.80[AMR][1000 genomes]
rs38001	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs38002	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs38003	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs38004	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs38011	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38012	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs38013	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38014	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs38016	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs38017	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs38018	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs38019	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38021	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38022	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs38023	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4236406	0.80[AFR][1000 genomes]
rs4720761	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4725057	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4725060	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4725065	0.95[ASN][1000 genomes]
rs62433404	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7785493	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9692283	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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	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
2	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
3	nsv519058	chr7:8094604-8115794	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1020686	chr7:8095118-8311985	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv538723	chr7:8095118-8311985	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2079853	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8047600-8108200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:8065000-8108600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:8066400-8127600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr7:8066600-8126000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:8066800-8108600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:8067000-8135400	Weak transcription	Pancreas	Pancrea
7	chr7:8075000-8108600	Weak transcription	Psoas Muscle	Psoas
8	chr7:8075000-8125800	Weak transcription	Lung	lung
9	chr7:8075000-8126800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:8075600-8104400	Weak transcription	HMEC	breast
11	chr7:8075600-8105000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr7:8075600-8113000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:8075600-8131800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:8076000-8111800	Weak transcription	Fetal Brain Male	brain
15	chr7:8076000-8124200	Weak transcription	Fetal Kidney	kidney
16	chr7:8076200-8108400	Weak transcription	Brain Angular Gyrus	brain
17	chr7:8077200-8106800	Weak transcription	Fetal Heart	heart
18	chr7:8085200-8109000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:8085200-8128400	Weak transcription	Small Intestine	intestine
20	chr7:8088600-8104400	Weak transcription	NH-A	brain
21	chr7:8088600-8108400	Weak transcription	Brain Substantia Nigra	brain
22	chr7:8088600-8108600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:8091400-8105000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr7:8091400-8127800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:8091800-8105000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:8092000-8105000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:8092000-8108600	Weak transcription	Right Ventricle	heart
28	chr7:8092400-8108600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:8092600-8108600	Weak transcription	Right Atrium	heart
30	chr7:8094000-8127800	Weak transcription	HSMM	muscle
31	chr7:8095200-8108600	Weak transcription	Left Ventricle	heart
32	chr7:8095200-8125800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr7:8095400-8129600	Weak transcription	Gastric	stomach
34	chr7:8095600-8108600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr7:8095800-8108600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:8096000-8104400	Weak transcription	Aorta	Aorta
37	chr7:8096000-8108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr7:8096000-8125800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr7:8096000-8127600	Weak transcription	Esophagus	oesophagus
40	chr7:8096000-8151600	Weak transcription	Spleen	Spleen
41	chr7:8096200-8106200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr7:8096200-8108400	Weak transcription	Fetal Muscle Leg	muscle
43	chr7:8096400-8108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:8097000-8104400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:8097200-8108200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr7:8097200-8114400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr7:8097400-8106600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr7:8097400-8124600	Weak transcription	Fetal Intestine Large	intestine
49	chr7:8099200-8113200	Strong transcription	Primary B cells from cord blood	blood
50	chr7:8100200-8108400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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